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change help section text
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SantaMcCloud committed Jan 15, 2025
1 parent 7783e4d commit 26258c9
Showing 1 changed file with 5 additions and 4 deletions.
9 changes: 5 additions & 4 deletions tools/binette/binette.xml
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help="Input at least 2 different contig tables. Look into the help section at the bottom for more information!"/>
<param argument="--contigs" type="data" format="fasta,fasta.gz" label="Input contig file"/>
<param argument="--proteins" type="data" format="fasta,fasta.gz" optional="true" label="Input FASTA file in Prodigal format (>contigID_geneID)"
help="If this file is provided all predicted genes contained in this file will be skiped. A example for this format is in the help section"/>
help="If this file is provided all predicted genes contained in this file will be skipped. A example for this format is in the help section"/>
<param argument="--min_completeness" type="integer" min="0" max="100" value="40" label="Set minimus completeness"
help="Threshold for bins for the final bin selection"/>
<param argument="--contamination_weight" type="integer" value="2" label="Set contamination weight"
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<options from_data_table="checkm2">
<filter type="sort_by" column="2"/>
</options>
<validator type="no_options" message="No databases are available for this version of Checkm2. Please contact the Galaxy adminstrators to request one be installed."/>
<validator type="no_options" message="No databases are available for this version of Checkm2. Please contact the Galaxy administrators to request one be installed."/>
</param>
</when>
</conditional>
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This file should contain all reads used to create the bins. The format of this file should be either fasta or fasta.gz.
- A CheckM2 dimaond databse
- A CheckM2 diamond database
.. class::infomark
This database can be download with using the CheckM2 package and the followed command: *checkm2 database --download --path <checkm2/database/>*. The format of this file is DMND.
This database can be download with using the CheckM2 package and the followed command: *checkm2 database --download --path <checkm2/database/>* or it is possible to use a database from the data manager.
- An optional (fasta/fasta.gz) file with predicted genes
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