Add 'metaQuantome function' workflow #628

clsiguret · 2024-12-10T14:16:37Z

We followed the recommendation to publish the workflow (licence, author list and email, steps annotations...)

Workflow imported from usegalaxy.eu using planemo workflow_test_init to use a valid invocation
Workflow tests passed using planemo test command on the usegalaxy.eu server
Readme.md written
CHANGELOG.md written
.dockstore.yml written

Thanks 😃

github-actions · 2024-12-10T14:36:53Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	2
Passed	1
Error	1
Failure	0
Skipped	0

Errored Tests

❌ metaproteomics_gtn_wf.ga_0

Execution Problem:

Failed to run workflow, at least one job is in [error] state.

Workflow invocation details

Invocation Messages

Steps

Step 1: Sixgill generated protein FASTA File:
- step_state: scheduled
Step 2: Dataset collection of MGF files:
- step_state: scheduled

Step 11: GO Terms: Biological Processes:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'biological_process'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 12: GO Terms: Cellular Localization:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'cellular_component'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 13: GO Terms: Molecular Functions:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"sqlite"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
sqlquery	`"SELECT go.description, \ncount(distinct bering_psms.sequence) as \"bering_peptides\", count(distinct bering_psms.id) as \"bering_psms\" \nFROM go JOIN bering_prot_go ON go.go_id = bering_prot_go.go_reference JOIN bering_prot on bering_prot_go.id = bering_prot.id JOIN bering_psms ON bering_prot.peptide = bering_psms.sequence\nWHERE go.aspect = 'molecular_function'\nGROUP BY go.description\nORDER BY bering_peptides desc,bering_psms desc"`

Step 3: Gene Ontology Terms (Selected):
- step_state: scheduled

Step 4: Search GUI:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir output; mkdir output_reports; cwd=`pwd`; export HOME=$cwd;  echo "" > searchgui_stderr &&  echo 'X!Tandem'; echo 'DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038';  echo 'searchgui.version=3.3.10' >> searchgui.properties;  ln -s -f '/tmp/tmpv70skkwu/files/c/e/5/dataset_ce50bcb9-4975-417d-84e2-ee8f2c929d82.dat' '2016_Jan_12_QE2_45.mgf'; echo 'Spectrums:2016_Jan_12_QE2_45.mgf(API:8f9493c490a360e6)'; ln -s -f '/tmp/tmpv70skkwu/files/8/8/c/dataset_88c47415-7a60-4c3a-ad2b-ce4318ab629a.dat' '2016_Jan_12_QE2_46.mgf'; echo 'Spectrums:2016_Jan_12_QE2_46.mgf(API:ccab57fcc7d711a8)'; ln -s -f '/tmp/tmpv70skkwu/files/6/6/3/dataset_66328c5f-02fc-485c-9e34-4de736abc5a4.dat' '2016_Jan_12_QE2_47.mgf'; echo 'Spectrums:2016_Jan_12_QE2_47.mgf(API:917490b19a919a3d)'; cp "/tmp/tmpv70skkwu/files/2/5/2/dataset_252e1b88-cd8b-4635-84a2-5511e5028573.dat" input_database.fasta;  echo 'Setting paths' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd -log $cwd/searchgui.log  2>> searchgui_stderr &&  echo 'Creating decoy database.' && searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="$cwd/bin" -in input_database.fasta -decoy  2>> searchgui_stderr && rm input_database.fasta && cp input_database_concatenated_target_decoy.fasta input_database.fasta &&  echo 'setting identification parameters' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI --exec_dir="$cwd/bin" -out SEARCHGUI_IdentificationParameters.par   -frag_tol '0.2' -frag_ppm '0' -prec_tol '10.0' -prec_ppm '1'  -min_charge 2 -max_charge 6 -fi b -ri y -min_isotope 0 -max_isotope 1 -enzyme "Trypsin" -mc "2"  -fixed_mods "Carbamidomethylation of C" -variable_mods "Oxidation of M"    -db input_database.fasta -useGeneMapping 0 -updateGeneMapping 0   -xtandem_npeaks 50 -xtandem_min_peaks 15 -xtandem_min_frag_mz 200 -xtandem_min_prec_mass 200 -xtandem_noise_suppr 1 -xtandem_dynamic_range 100 -xtandem_quick_acetyl 0 -xtandem_quick_pyro 0 -xtandem_stp_bias 0 -xtandem_evalue 100.0 -xtandem_output_proteins 0 -xtandem_output_sequences 0 -xtandem_output_spectra 1              2> searchgui_stderr) &&  echo 'running search gui' && (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI --exec_dir="$cwd/bin" -spectrum_files $cwd -output_folder $cwd/output -id_params SEARCHGUI_IdentificationParameters.par  -threads "${GALAXY_SLOTS:-12}"     -xtandem 1  -myrimatch 0  -msgf 0  -omssa 0  -comet 0  -tide 0  -ms_amanda 0  -andromeda 0  -novor 0  -directag 0  -output_option 0  -output_data 1  2>> searchgui_stderr)  &&  (mv output/searchgui_out.zip searchgui_out.zip 2>> searchgui_stderr)  &&  (zip -u searchgui_out.zip searchgui.properties 2>> searchgui_stderr);  cat searchgui_stderr 2>&1;

Exit Code:

```
0
```

Standard Output:

X!Tandem
DB: FASTA_Bering_Strait_Trimmed_metapeptides_cRAP.fasta sequences: 17038
Spectrums:2016_Jan_12_QE2_45.mgf(API:8f9493c490a360e6)
Spectrums:2016_Jan_12_QE2_46.mgf(API:ccab57fcc7d711a8)
Spectrums:2016_Jan_12_QE2_47.mgf(API:917490b19a919a3d)
Setting paths
Path configuration completed.
Creating decoy database.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90%Input: /tmp/tmpv70skkwu/job_working_directory/000/6/working/input_database.fasta

Name: input_database
Version: 10.12.2024
Decoy Tag: null
Type: Generic_Split_Header
Last modified: Tue Dec 10 14:26:48 GMT 2024
Size: 17038 sequences


Tue Dec 10 14:26:50 GMT 2024 Appending Decoy Sequences. Please Wait...
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%Reindexing: input_database_concatenated_target_decoy.fasta.

10% 20% 30% 40% 50% 60% 70% 80% 90%Decoy file successfully created: 

Output: /tmp/tmpv70skkwu/job_working_directory/000/6/working/input_database_concatenated_target_decoy.fasta

Name: input_database_concatenated_target_decoy
Version: 10.12.2024
Decoy Tag: REVERSED
Type: Generic_Split_Header
Last modified: Tue Dec 10 14:26:51 GMT 2024
Size: 34076 sequences (17038 target)

setting identification parameters
Reindexing: input_database.fasta.

Identification parameters file created: /tmp/tmpv70skkwu/job_working_directory/000/6/working/SEARCHGUI_IdentificationParameters.par

running search gui
Tue Dec 10 14:26:59 GMT 2024 Validating MGF file: /tmp/tmpv70skkwu/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Tue Dec 10 14:27:00 GMT 2024 Validating MGF file: /tmp/tmpv70skkwu/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%
Tue Dec 10 14:27:00 GMT 2024 Validating MGF file: /tmp/tmpv70skkwu/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf
10% 20% 30% 40% 50% 60% 70% 80% 90%

Tue Dec 10 14:27:01 GMT 2024 Indexing spectrum files.
Tue Dec 10 14:27:01 GMT 2024 Extracting search settings.



Processing: 2016_Jan_12_QE2_45.mgf (1/3)


xtandem command: 
/tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Tue Dec 10 14:27:01 GMT 2024 Processing 2016_Jan_12_QE2_45.mgf with X!Tandem.

/tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Tue Dec 10 14:27:01 GMT 2024 X!Tandem finished for /tmp/tmpv70skkwu/job_working_directory/000/6/working/2016_Jan_12_QE2_45.mgf (10.0 milliseconds).

Tue Dec 10 14:27:01 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_45.mgf.
Tue Dec 10 14:27:01 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_45.mgf.


Processing: 2016_Jan_12_QE2_47.mgf (2/3)


xtandem command: 
/tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Tue Dec 10 14:27:01 GMT 2024 Processing 2016_Jan_12_QE2_47.mgf with X!Tandem.

/tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Tue Dec 10 14:27:01 GMT 2024 X!Tandem finished for /tmp/tmpv70skkwu/job_working_directory/000/6/working/2016_Jan_12_QE2_47.mgf (1.0 milliseconds).

Tue Dec 10 14:27:01 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_47.mgf.
Tue Dec 10 14:27:01 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_47.mgf.


Processing: 2016_Jan_12_QE2_46.mgf (3/3)


xtandem command: 
/tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem /tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/input_searchGUI.xml 

Tue Dec 10 14:27:01 GMT 2024 Processing 2016_Jan_12_QE2_46.mgf with X!Tandem.

/tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/resources/XTandem/linux/linux_64bit/tandem: error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory


Tue Dec 10 14:27:01 GMT 2024 X!Tandem finished for /tmp/tmpv70skkwu/job_working_directory/000/6/working/2016_Jan_12_QE2_46.mgf (1.0 milliseconds).

Tue Dec 10 14:27:01 GMT 2024 Could not rename X!Tandem result for 2016_Jan_12_QE2_46.mgf.
Tue Dec 10 14:27:01 GMT 2024 Could not find X!Tandem result file for 2016_Jan_12_QE2_46.mgf.
Tue Dec 10 14:27:01 GMT 2024 Zipping output files.

10% 20% 30% 40% 50% 60% 70% 80% 90%
Tue Dec 10 14:27:02 GMT 2024 Search Completed (971.0 milliseconds).



Search Completed.

  adding: searchgui.properties (stored 0%)
Reindexing: input_database.fasta. (changes in the file detected)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.gson.internal.bind.ReflectiveTypeAdapterFactory (file:/tmp/tmpv70skkwu/job_working_directory/000/6/working/bin/lib/gson-2.4.jar) to field java.awt.Color.value
WARNING: Please consider reporting this to the maintainers of com.google.gson.internal.bind.ReflectiveTypeAdapterFactory
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"fasta"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
advanced_options	{"comet": {"__current_case__": 0, "comet_advanced": "no"}, "directtag": {"__current_case__": 0, "directtag_advanced": "no"}, "ms_amanda": {"__current_case__": 0, "ms_amanda_advanced": "no"}, "msgf": {"__current_case__": 0, "msgf_advanced": "no"}, "myrimatch": {"__current_case__": 0, "myrimatch_advanced": "no"}, "novor": {"__current_case__": 0, "novor_advanced": "no"}, "omssa": {"__current_case__": 0, "omssa_advanced": "no"}, "searchgui_advanced": {"__current_case__": 0, "searchgui_advanced_selector": "basic"}, "tide": {"__current_case__": 0, "tide_advanced": "no"}, "xtandem": {"__current_case__": 1, "xtandem_advanced": "yes", "xtandem_dynamic_range": "100", "xtandem_evalue": "100.0", "xtandem_min_frag_mz": "200", "xtandem_min_peaks": "15", "xtandem_min_prec_mass": "200", "xtandem_noise_suppr": true, "xtandem_npeaks": "50", "xtandem_output_proteins": false, "xtandem_output_sequences": false, "xtandem_output_spectra": true, "xtandem_quick_acetyl": false, "xtandem_quick_pyro": false, "xtandem_refine": {"__current_case__": 0, "xtandem_refine_selector": "no"}, "xtandem_stp_bias": false}}
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
precursor_options	`{"forward_ion": "b", "fragment_tol": "0.2", "fragment_tol_units": "0", "max_charge": "6", "max_isotope": "1", "min_charge": "2", "min_isotope": "0", "precursor_ion_tol": "10.0", "precursor_ion_tol_units": "1", "reverse_ion": "y"}`
protein_database_options	`{"create_decoy": true, "update_gene_mapping": false, "use_gene_mapping": false}`
protein_digest_options	`{"digestion": {"__current_case__": 0, "cleavage": "0", "digests": [{"__index__": 0, "enzyme": "Trypsin", "missed_cleavages": "2"}]}}`
protein_modification_options	`{"fixed_modifications": ["Carbamidomethylation of C"], "variable_modifications": ["Oxidation of M"]}`
search_engines_options	`{"engines": ["X!Tandem"]}`

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/peptideshaker/peptide_shaker/1.16.36.3:

step_state: scheduled

Jobs

Job 1:

Job state is error

Command Line:

mkdir output_reports && cwd=`pwd` && export HOME=$cwd &&  echo "" > peptideshaker_stderr &&  ln -s '/tmp/tmpv70skkwu/files/4/e/0/dataset_4e01e372-b435-406f-9c50-1827382a665a.dat' searchgui_input.zip && jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&   peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI --exec_dir="$cwd/bin" -temp_folder $cwd/PathSettingsCLI -log $cwd/peptideshaker.log &&   (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI --exec_dir="$cwd/bin" -gui 0 -temp_folder $cwd/PeptideShakerCLI -experiment 'Galaxy_Experiment_2024121014271733840827' -sample 'Sample_2024121014271733840827' -replicate 1 -identification_files $cwd/searchgui_input.zip -id_params $cwd/SEARCHGUI_IdentificationParameters.par -out $cwd/peptideshaker_output.cpsx -threads "${GALAXY_SLOTS:-12}"   -import_peptide_length_min "6" -import_peptide_length_max "30" -import_precurosor_mz "10.0" -import_precurosor_mz_ppm "0" -exclude_unknown_ptms "1"   -output_file $cwd/output.mzid -include_sequences 0 -contact_first_name "Proteomics" -contact_last_name "Galaxy" -contact_email "[email protected]" -contact_address "[email protected]" -organization_name "University of Minnesota" -organization_email "[email protected]" -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"  -out_reports $cwd/output_reports -reports 3,6,0,9  2>> peptideshaker_stderr)   && find $cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \; && find $cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \; && find $cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \; && find $cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;  && cat peptideshaker_stderr 2>&1;

Exit Code:

```
1
```

Standard Output:

 inflated: SEARCHGUI_IdentificationParameters.par
Path configuration completed.
Path configuration completed.
Tue Dec 10 14:27:28 GMT 2024 Unzipping searchgui_input.zip.
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Tue Dec 10 14:27:28 GMT 2024 Import process for Galaxy_Experiment_2024121014271733840827 (Sample: Sample_2024121014271733840827, Replicate: 1)

Tue Dec 10 14:27:28 GMT 2024 Importing sequences from input_database.fasta.
Reindexing: input_database.fasta.
10% 20% 30% 40% 50% 60% 70% 80% 90% 0%
10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
Tue Dec 10 14:27:34 GMT 2024 FASTA file import completed.
Tue Dec 10 14:27:34 GMT 2024 Establishing local database connection.
Tue Dec 10 14:27:36 GMT 2024 Reading identification files.
Tue Dec 10 14:27:36 GMT 2024 No identifications retained.
Tue Dec 10 14:27:36 GMT 2024 PeptideShaker Processing Canceled.
<CompomicsError>PeptideShaker processing canceled. Please see the PeptideShaker log file: /tmp/tmpv70skkwu/job_working_directory/000/7/working/bin/resources/PeptideShaker.log</CompomicsError>

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"searchgui_archive"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
contact_options	`{"__current_case__": 0, "contact_options_selector": "no"}`
dbkey	`"?"`
exporting_options	`{"mzidentml_conditional": {"__current_case__": 0, "include_sequences": false, "mzidentml_creation": true}, "output_reports": ["3", "6", "9", "0"], "zip_conditional": {"__current_case__": 0, "export_cps": false, "zip_output_boolean": false}}`
filtering_options	`{"__current_case__": 1, "exclude_unknown_ptms": true, "filtering_options_selector": "yes", "max_peptide_length": "30", "max_precursor_error": "10.0", "max_precursor_error_type": "0", "min_peptide_length": "6"}`
processing_options	`{"__current_case__": 0, "processing_options_selector": "no"}`

Step 6: Query Tabular Select Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 1, "header": "no"}`
save_db	`false`
sqlquery	`"SELECT distinct sequence \nFROM psm \nWHERE confidence >= 95 \nORDER BY sequence"`
tables	`[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}]`
workdb	`"workdb.sqlite"`

Step 7: Unipept pept2prot:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`"tsv"`
strict	`false`
unipept	`{"__current_case__": 2, "api": "pept2prot", "equate_il": true, "extra": true}`

Step 8: Unipept lca:

step_state: scheduled

Jobs

Job 1:

Job state is new

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
peptide_src	`{"__current_case__": 1, "column": "1", "fmt": "tabular", "input_tsv": {"values": [{"id": 12, "src": "hda"}]}}`
selected_outputs	`["tsv", "json", "ec_json"]`
strict	`false`
unipept	`{"__current_case__": 0, "allfields": false, "api": "pept2lca", "equate_il": false, "extra": false, "names": true}`

Step 9: Go Pop2Prot DB:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`true`
sqlquery	`"SELECT sequence as \"peptide\", count(id) as \"PSMs\"\nFROM bering_psms\nWHERE confidence >= 95\nGROUP BY sequence\nORDER BY sequence\n"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}]}, "table": {"values": [{"id": 5, "src": "hda"}]}, "tbl_opts": {"col_names": "aspect,go_id,description", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "aspect,go_id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "go"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,peptide,uniprot_id,taxon_id,taxon_name,ec_references,go_references,refseq_ids,refseq_protein_ids,insdc_ids,insdc_protein_ids", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "id,peptide", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot"}}, {"__index__": 2, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 0, "filter_type": "skip", "skip_lines": "1"}}, {"__index__": 1, "filter": {"__current_case__": 2, "filter_type": "prepend_line_num"}}, {"__index__": 2, "filter": {"__current_case__": 7, "columns": "1,7", "filter_type": "select_columns"}}, {"__index__": 3, "filter": {"__current_case__": 9, "columns": "2", "filter_type": "normalize", "separator": " "}}]}, "table": {"values": [{"id": 13, "src": "hda"}]}, "tbl_opts": {"col_names": "id,go_reference", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "go_reference,id", "unique": false}], "load_named_columns": false, "pkey_autoincr": "", "table_name": "bering_prot_go"}}, {"__index__": 3, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}, {"__index__": 1, "filter": {"__current_case__": 7, "columns": "1,3,23,24", "filter_type": "select_columns"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": "id,sequence,confidence,validation", "column_names_from_first_line": false, "indexes": [{"__index__": 0, "index_columns": "sequence,id", "unique": false}], "load_named_columns": true, "pkey_autoincr": "", "table_name": "bering_psms"}}]
workdb	`"workdb.sqlite"`

Step 10: Genera | PSMs | Peptides:

step_state: scheduled

Jobs

Job 1:

Job state is paused

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"b69b558ab70211ef899e7c1e521b5a05"`
add_to_database	`{"withdb": null}`
addqueries	`{"queries": []}`
chromInfo	`"/tmp/tmpv70skkwu/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
modify_database	`{"sql_stmts": []}`
query_result	`{"__current_case__": 0, "header": "yes", "header_prefix": "35"}`
save_db	`false`
sqlquery	`"SELECT lca.genus,count(psm.sequence) as \"PSMs\",count(distinct psm.sequence) as \"DISTINCT PEPTIDES\" \nFROM psm LEFT JOIN lca ON psm.sequence = lca.peptide \nWHERE confidence >= 95 \nGROUP BY lca.genus \nORDER BY PSMs desc, 'DISTINCT PEPTIDES' desc"`
tables	[{"__index__": 0, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "include_match", "regex_pattern": "^\\d"}}]}, "table": {"values": [{"id": 9, "src": "hda"}]}, "tbl_opts": {"col_names": ",,sequence,,,,,,,,,,,,,,,,,,,,confidence,validation", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "psm"}}, {"__index__": 1, "input_opts": {"linefilters": [{"__index__": 0, "filter": {"__current_case__": 6, "filter_type": "regex", "regex_action": "exclude_match", "regex_pattern": "#peptide"}}]}, "table": {"values": [{"id": 15, "src": "hda"}]}, "tbl_opts": {"col_names": "peptide,,,,,,,,,,,,,,,,,,,,,genus", "column_names_from_first_line": false, "indexes": [], "load_named_columns": true, "pkey_autoincr": "", "table_name": "lca"}}]
workdb	`"workdb.sqlite"`

Other invocation details
- error_message
  - Failed to run workflow, at least one job is in [error] state.
- history_id
  - 087901daf3db8d70
- history_state
  - error
- invocation_id
  - 087901daf3db8d70
- invocation_state
  - scheduled
- workflow_id
  - 087901daf3db8d70

Passed Tests

✅ metaquantome_function_wf.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_db/metaquantome_db/2.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p data && metaquantome db 'ncbi' --dir data && metaquantome db 'go' --dir data && metaquantome db 'ec' --dir data && tar --create --file '/tmp/tmp1jwn7mhg/job_working_directory/000/3/outputs/dataset_f7bb5520-7e16-4bd3-9097-91a6d2f28679.dat' data

Exit Code:

```
0
```

Standard Error:

NCBI database format is outdated. Upgrading
Downloading taxdump.tar.gz from NCBI FTP site (via HTTP)...
Done. Parsing...

Inserting synonyms:          0 
Inserting synonyms:       5000 
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Inserting synonyms:      370000 
Inserting synonyms:      375000 
Inserting taxid merges:      0 
Inserting taxid merges:   5000 
Inserting taxid merges:  10000 
Inserting taxid merges:  15000 
Inserting taxid merges:  20000 
Inserting taxid merges:  25000 
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Inserting taxids:           0 
Inserting taxids:        5000 
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Inserting taxids:       2455000 
Inserting taxids:       2460000 
Inserting taxids:       2465000 
Inserting taxids:       2470000 
Inserting taxids:       2475000 
Inserting taxids:       2480000 
Inserting taxids:       2485000 
Inserting taxids:       2490000 
Inserting taxids:       2495000 
Inserting taxids:       2500000 
Inserting taxids:       2505000 
Inserting taxids:       2510000 
Inserting taxids:       2515000 
Inserting taxids:       2520000 
Inserting taxids:       2525000 
Inserting taxids:       2530000 
Inserting taxids:       2535000 
Inserting taxids:       2540000 
Inserting taxids:       2545000 
Inserting taxids:       2550000 
Inserting taxids:       2555000 
Inserting taxids:       2560000 
Inserting taxids:       2565000 
Inserting taxids:       2570000 
Inserting taxids:       2575000 
Inserting taxids:       2580000 
Inserting taxids:       2585000 
Inserting taxids:       2590000 
Inserting taxids:       2595000 
Inserting taxids:       2600000 
Inserting taxids:       2605000 
Inserting taxids:       2610000 
Inserting taxids:       2615000 
Inserting taxids:       2620000 
Inserting taxids:       2625000 
Inserting taxids:       2630000 Downloading full GO obo file from http://purl.obolibrary.org/obo/go/go-basic.obo to data/go-basic.obo
Downloading generic slim GO obo file from http://current.geneontology.org/ontology/subsets/goslim_metagenomics.obo to data/goslim_metagenomics.obo
Downloading enzyme files from ftp.expasy.org to data

Standard Output:

Loading node names...
2632321 names loaded.
378267 synonyms loaded.
Loading nodes...
2632321 nodes loaded.
Linking nodes...
Tree is loaded.
Updating database: data/taxa.sqlite ...

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Uploading to data/taxa.sqlite

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
databases	`["ncbi", "go", "ec"]`
dbkey	`"?"`

Step 2: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_sample/metaquantome_sample/2.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

echo -e 'group	colnames' > samp_file.tab; echo -e 'T2	T2_A1,T2_B1' >> samp_file.tab; echo -e 'T4	T4A_1,T4B_1' >> samp_file.tab; echo -e 'T7	T7A_1,T7B_1' >> samp_file.tab;

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"data"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
samps_args	`{"__current_case__": 0, "samps": [{"__index__": 0, "col_names": "T2_A1,T2_B1", "group_name": "T2"}, {"__index__": 1, "col_names": "T4A_1,T4B_1", "group_name": "T4"}, {"__index__": 2, "col_names": "T7A_1,T7B_1", "group_name": "T7"}], "samps_src": "build"}`

Step 11: T7-T2-Volcano-Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp1jwn7mhg/files/2/c/6/dataset_2c6c7564-85c5-4bbc-9a91-36eea8e7aa0c.dat' 'metaQuantome__stat_on_data_6_and_data_4_stats' && metaquantome viz --samps '/tmp/tmp1jwn7mhg/files/1/0/1/dataset_101b18bb-4f55-43fb-93b6-dafa0da9206b.dat' --mode 'f' --ontology='go' --infile='metaQuantome__stat_on_data_6_and_data_4_stats' --plottype='volcano' --fc_name='log2fc_T7_over_T2' --fc_corr_p='corrected_p_T7_over_T2' --textannot='id'  --gosplit --img='outfile.png' --tabfile='plotdata.tab' && mkdir '/tmp/tmp1jwn7mhg/job_working_directory/000/11/outputs/dataset_ea48032a-207f-47fa-97bb-3e8335c02aca_files' && cp outfile.png '/tmp/tmp1jwn7mhg/job_working_directory/000/11/outputs/dataset_ea48032a-207f-47fa-97bb-3e8335c02aca_files' && echo "<!DOCTYPE html> <html> <body> <img src=\"outfile.png\" width=600> <br> <p>To download the image, right-click and choose \"Save image as...\"</p> <br> <p> If text is cut off or the plot is not displaying properly, the easiest fix is to increase the plot dimensions </p> </body> </html>" > wrapped_outfile.html && if test -f 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' feature_cluster_data.txt; fi && if test -f 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' sample_cluster_data.txt; fi && if test -f 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt' PC_Data.txt; fi

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
height	`None`
mode_args	`{"__current_case__": 0, "mode": "f", "ontology": "go", "plot": {"__current_case__": 1, "fc_corr_p": "corrected_p_T7_over_T2", "fc_name": "log2fc_T7_over_T2", "flip_fc": false, "gosplit": true, "plottype": "volcano", "textannot": "id"}}`
width	`None`

Step 12: T4-T2-Volcano-Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp1jwn7mhg/files/2/c/6/dataset_2c6c7564-85c5-4bbc-9a91-36eea8e7aa0c.dat' 'metaQuantome__stat_on_data_6_and_data_4_stats' && metaquantome viz --samps '/tmp/tmp1jwn7mhg/files/1/0/1/dataset_101b18bb-4f55-43fb-93b6-dafa0da9206b.dat' --mode 'f' --ontology='go' --infile='metaQuantome__stat_on_data_6_and_data_4_stats' --plottype='volcano' --fc_name='log2fc_T4_over_T2' --fc_corr_p='corrected_p_T4_over_T2' --textannot='id'  --gosplit --img='outfile.png' --tabfile='plotdata.tab' && mkdir '/tmp/tmp1jwn7mhg/job_working_directory/000/12/outputs/dataset_3976ff39-1256-44d3-8cd0-122cf1cd0588_files' && cp outfile.png '/tmp/tmp1jwn7mhg/job_working_directory/000/12/outputs/dataset_3976ff39-1256-44d3-8cd0-122cf1cd0588_files' && echo "<!DOCTYPE html> <html> <body> <img src=\"outfile.png\" width=600> <br> <p>To download the image, right-click and choose \"Save image as...\"</p> <br> <p> If text is cut off or the plot is not displaying properly, the easiest fix is to increase the plot dimensions </p> </body> </html>" > wrapped_outfile.html && if test -f 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' feature_cluster_data.txt; fi && if test -f 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' sample_cluster_data.txt; fi && if test -f 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt' PC_Data.txt; fi

Exit Code:

```
0
```

Standard Error:

Warning message:
Removed 3 rows containing missing values (geom_hline).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
height	`None`
mode_args	`{"__current_case__": 0, "mode": "f", "ontology": "go", "plot": {"__current_case__": 1, "fc_corr_p": "corrected_p_T4_over_T2", "fc_name": "log2fc_T4_over_T2", "flip_fc": false, "gosplit": true, "plottype": "volcano", "textannot": "id"}}`
width	`None`

Step 3: Functional file:
- step_state: scheduled
Step 4: Intensity file:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_expand/metaquantome_expand/2.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

tar -xf '/tmp/tmp1jwn7mhg/files/f/7/b/dataset_f7bb5520-7e16-4bd3-9097-91a6d2f28679.dat' && metaquantome expand --data_dir ./data --samps '/tmp/tmp1jwn7mhg/files/1/0/1/dataset_101b18bb-4f55-43fb-93b6-dafa0da9206b.dat' --mode 'f' --int_file='/tmp/tmp1jwn7mhg/files/0/f/a/dataset_0fac3f4e-0713-4ec0-b10d-92404182dbda.dat' --pep_colname_int='peptide'  --func_file='/tmp/tmp1jwn7mhg/files/d/4/5/dataset_d4561c5a-43f8-4dca-b9e6-6d24dced1614.dat' --pep_colname_func='peptide'   --func_colname='go_term'   --ontology='go'  --outfile='/tmp/tmp1jwn7mhg/job_working_directory/000/5/outputs/dataset_aa611c07-d518-49d3-a7c8-e2bbed34ff62.dat'

Exit Code:

```
0
```

Standard Output:

load obo file ./data/go-basic.obo
./data/go-basic.obo: fmt(1.2) rel(2024-10-27) 44,017 GO Terms

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tar"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_args	`{"__current_case__": 0, "func_colname": "go_term", "func_file": {"values": [{"id": 1, "src": "hda"}]}, "mode": "f", "ontology_args": {"__current_case__": 0, "ontology": "go", "slim_down": false}, "pep_colname_func": "peptide"}`
pep_colname_int	`"peptide"`

Step 6: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_filter/metaquantome_filter/2.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

metaquantome filter --samps '/tmp/tmp1jwn7mhg/files/1/0/1/dataset_101b18bb-4f55-43fb-93b6-dafa0da9206b.dat' --mode 'f' --ontology='go' --expand_file '/tmp/tmp1jwn7mhg/files/a/a/6/dataset_aa611c07-d518-49d3-a7c8-e2bbed34ff62.dat' --min_peptides 1 --min_pep_nsamp 1 --min_children_non_leaf 2 --min_child_nsamp 1 --qthreshold 2 --outfile='/tmp/tmp1jwn7mhg/job_working_directory/000/6/outputs/dataset_602d8692-473a-45d7-a652-6988d0151cf3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
min_child_nsamp	`"1"`
min_children_non_leaf	`"2"`
min_pep_nsamp	`"1"`
min_peptides	`"1"`
mode_args	`{"__current_case__": 0, "mode": "f", "ontology_args": {"__current_case__": 0, "ontology": "go", "slim_down": false}}`
qthreshold	`"2"`

Step 7: toolshed.g2.bx.psu.edu/repos/galaxyp/metaquantome_stat/metaquantome_stat/2.0.2+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

metaquantome stat --samps '/tmp/tmp1jwn7mhg/files/1/0/1/dataset_101b18bb-4f55-43fb-93b6-dafa0da9206b.dat' --mode 'f' --ontology='go' --file '/tmp/tmp1jwn7mhg/files/6/0/2/dataset_602d8692-473a-45d7-a652-6988d0151cf3.dat' --control_group 'T2' --parametric 'True' --paired --outfile='/tmp/tmp1jwn7mhg/job_working_directory/000/7/outputs/dataset_2c6c7564-85c5-4bbc-9a91-36eea8e7aa0c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
control_group	`"T2"`
dbkey	`"?"`
mode_args	`{"__current_case__": 0, "mode": "f", "ontology_args": {"__current_case__": 0, "ontology": "go", "slim_down": false}}`
paired	`true`
parametric	`"True"`

Step 8: T2-Bar-Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp1jwn7mhg/files/2/c/6/dataset_2c6c7564-85c5-4bbc-9a91-36eea8e7aa0c.dat' 'metaQuantome__stat_on_data_6_and_data_4_stats' && metaquantome viz --samps '/tmp/tmp1jwn7mhg/files/2/c/6/dataset_2c6c7564-85c5-4bbc-9a91-36eea8e7aa0c.dat' --mode 'f' --ontology='go' --infile='metaQuantome__stat_on_data_6_and_data_4_stats' --plottype='bar' --meancol='T2_mean' --nterms=5 --target_onto='mf' --barcol=2 --img='outfile.png' --tabfile='plotdata.tab' && mkdir '/tmp/tmp1jwn7mhg/job_working_directory/000/8/outputs/dataset_f999f2be-ef36-4704-b378-bce979dc6e0d_files' && cp outfile.png '/tmp/tmp1jwn7mhg/job_working_directory/000/8/outputs/dataset_f999f2be-ef36-4704-b378-bce979dc6e0d_files' && echo "<!DOCTYPE html> <html> <body> <img src=\"outfile.png\" width=600> <br> <p>To download the image, right-click and choose \"Save image as...\"</p> <br> <p> If text is cut off or the plot is not displaying properly, the easiest fix is to increase the plot dimensions </p> </body> </html>" > wrapped_outfile.html && if test -f 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' feature_cluster_data.txt; fi && if test -f 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' sample_cluster_data.txt; fi && if test -f 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt' PC_Data.txt; fi

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
height	`None`
mode_args	`{"__current_case__": 0, "mode": "f", "ontology": "go", "plot": {"__current_case__": 0, "barcol": "2", "meancol": "T2_mean", "nterms": "5", "plottype": "bar", "target_onto": "mf"}}`
width	`None`

Step 9: T4-Bar-Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp1jwn7mhg/files/2/c/6/dataset_2c6c7564-85c5-4bbc-9a91-36eea8e7aa0c.dat' 'metaQuantome__stat_on_data_6_and_data_4_stats' && metaquantome viz --samps '/tmp/tmp1jwn7mhg/files/1/0/1/dataset_101b18bb-4f55-43fb-93b6-dafa0da9206b.dat' --mode 'f' --ontology='go' --infile='metaQuantome__stat_on_data_6_and_data_4_stats' --plottype='bar' --meancol='T4_mean' --nterms=5 --target_onto='mf' --barcol=2 --img='outfile.png' --tabfile='plotdata.tab' && mkdir '/tmp/tmp1jwn7mhg/job_working_directory/000/9/outputs/dataset_12c184fc-eee9-4bda-b75c-df1fb62ad851_files' && cp outfile.png '/tmp/tmp1jwn7mhg/job_working_directory/000/9/outputs/dataset_12c184fc-eee9-4bda-b75c-df1fb62ad851_files' && echo "<!DOCTYPE html> <html> <body> <img src=\"outfile.png\" width=600> <br> <p>To download the image, right-click and choose \"Save image as...\"</p> <br> <p> If text is cut off or the plot is not displaying properly, the easiest fix is to increase the plot dimensions </p> </body> </html>" > wrapped_outfile.html && if test -f 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' feature_cluster_data.txt; fi && if test -f 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' sample_cluster_data.txt; fi && if test -f 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt' PC_Data.txt; fi

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
height	`None`
mode_args	`{"__current_case__": 0, "mode": "f", "ontology": "go", "plot": {"__current_case__": 0, "barcol": "2", "meancol": "T4_mean", "nterms": "5", "plottype": "bar", "target_onto": "mf"}}`
width	`None`

Step 10: T7-Bar-Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -s '/tmp/tmp1jwn7mhg/files/2/c/6/dataset_2c6c7564-85c5-4bbc-9a91-36eea8e7aa0c.dat' 'metaQuantome__stat_on_data_6_and_data_4_stats' && metaquantome viz --samps '/tmp/tmp1jwn7mhg/files/1/0/1/dataset_101b18bb-4f55-43fb-93b6-dafa0da9206b.dat' --mode 'f' --ontology='go' --infile='metaQuantome__stat_on_data_6_and_data_4_stats' --plottype='bar' --meancol='T7_mean' --nterms=5 --target_onto='mf' --barcol=2 --img='outfile.png' --tabfile='plotdata.tab' && mkdir '/tmp/tmp1jwn7mhg/job_working_directory/000/10/outputs/dataset_71e085b1-2c11-405b-8f20-63ed680d2363_files' && cp outfile.png '/tmp/tmp1jwn7mhg/job_working_directory/000/10/outputs/dataset_71e085b1-2c11-405b-8f20-63ed680d2363_files' && echo "<!DOCTYPE html> <html> <body> <img src=\"outfile.png\" width=600> <br> <p>To download the image, right-click and choose \"Save image as...\"</p> <br> <p> If text is cut off or the plot is not displaying properly, the easiest fix is to increase the plot dimensions </p> </body> </html>" > wrapped_outfile.html && if test -f 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'feature_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' feature_cluster_data.txt; fi && if test -f 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'sample_cluster_metaQuantome: stat on data 6 and data 4 stats.txt' sample_cluster_data.txt; fi && if test -f 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt'; then mv 'PC_Data_metaQuantome: stat on data 6 and data 4 stats.txt' PC_Data.txt; fi

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f56870aeb70211ef84db0022480419c4"`
chromInfo	`"/tmp/tmp1jwn7mhg/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
height	`None`
mode_args	`{"__current_case__": 0, "mode": "f", "ontology": "go", "plot": {"__current_case__": 0, "barcol": "2", "meancol": "T7_mean", "nterms": "5", "plottype": "bar", "target_onto": "mf"}}`
width	`None`

Other invocation details
- history_id
  - 3d86a2a54bdc44f7
- history_state
  - ok
- invocation_id
  - 3d86a2a54bdc44f7
- invocation_state
  - scheduled
- workflow_id
  - 3d86a2a54bdc44f7

mvdbeek · 2024-12-11T14:19:39Z

workflows/proteomics/metaquantome-function/metaquantome_function_wf-tests.yml

+      asserts:
+        has_text: 
+          text: "GO:0000015"
+    Bar plot data for sample T2:


What's sample T2 / T4 / T7 ?

wm75 · 2024-12-11T16:20:36Z

More input/output and analysis description is required in the README and as part of input annotations for me to review this properly.

workflows/proteomics/metaquantome-function/README.md

workflows/proteomics/metaquantome-function/metaquantome_function_wf.ga

wm75 · 2024-12-11T16:18:14Z

workflows/proteomics/metaquantome-function/metaquantome_function_wf.ga

+                "owner": "galaxyp",
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            },
+            "tool_state": "{\"samps_args\": {\"samps_src\": \"build\", \"__current_case__\": 0, \"samps\": [{\"__index__\": 0, \"group_name\": \"T2\", \"col_names\": \"T2_A1,T2_B1\"}, {\"__index__\": 1, \"group_name\": \"T4\", \"col_names\": \"T4A_1,T4B_1\"}, {\"__index__\": 2, \"group_name\": \"T7\", \"col_names\": \"T7A_1,T7B_1\"}]}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",


This step is strange. Why tie a general WF to specific sample and group names? All of these should probably be WF input params.

workflows/proteomics/metaquantome-function/metaquantome_function_wf.ga

…on_wf.ga Co-authored-by: Wolfgang Maier <[email protected]>

WF steps outlined

clsiguret added 3 commits December 10, 2024 11:39

Init metaproteomics-gtn

049395a

init metaquantome-function workflow

8f0e4a9

clean repo

28ee074

mvdbeek reviewed Dec 11, 2024

View reviewed changes

wm75 reviewed Dec 11, 2024

View reviewed changes

wm75 mentioned this pull request Dec 11, 2024

Add 'metaQuantome Taxonomy' workflow #630

Open

5 tasks

meltemktn and others added 4 commits December 12, 2024 23:43

Update workflows/proteomics/metaquantome-function/metaquantome_functi…

cce125b

…on_wf.ga Co-authored-by: Wolfgang Maier <[email protected]>

Update README.md

1cd3907

WF steps outlined

Update README.md

06581d7

Update info for inputs

732954e

Provide feedback

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Add 'metaQuantome function' workflow #628

Add 'metaQuantome function' workflow #628

clsiguret commented Dec 10, 2024 •

edited

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github-actions bot commented Dec 10, 2024

Workflow invocation details

Workflow invocation details

mvdbeek Dec 11, 2024

wm75 commented Dec 11, 2024

wm75 Dec 11, 2024

Add 'metaQuantome function' workflow #628

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Add 'metaQuantome function' workflow #628

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clsiguret commented Dec 10, 2024 • edited Loading

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Test Results (powered by Planemo)

Test Summary

Workflow invocation details

Workflow invocation details

mvdbeek Dec 11, 2024

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wm75 commented Dec 11, 2024

wm75 Dec 11, 2024

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clsiguret commented Dec 10, 2024 •

edited

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