removed input oddities - READY?

galaxyproject · Jan 15, 2025 · d73eeec · d73eeec
1 parent 1107d31
commit d73eeec
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Showing 2 changed files with 12 additions and 16 deletions.
diff --git a/tools/squirrel/squirrel-phylo.xml b/tools/squirrel/squirrel-phylo.xml
@@ -7,19 +7,17 @@
     <expand macro="version_command"/>
 
     <command detect_errors="exit_code"><![CDATA[
-      #set $input_file_name = str($sequences.element_identifier).replace(".fasta", "")
-      #set $linked_input = str($input_file_name) + '.fasta'
-      #set $alignment_output = str($input_file_name) + '.aln.fasta'
-      #set $tree_output = str($input_file_name) + '.tree'
+      #set $alignment_output = 'input.aln.fasta'
+      #set $tree_output = 'input.tree'
 
       #if $apobec3
-        #set $aa_recon_output = str($input_file_name) + ".tree.amino_acid.reconstruction.csv"
-        #set $branch_snps_output = str($input_file_name) + ".tree.branch_snps.reconstruction.csv"
-        #set $svg_output = str($input_file_name) + ".tree.svg"
-        #set $png_output = str($input_file_name) + ".tree.png"
+        #set $aa_recon_output = "input.tree.amino_acid.reconstruction.csv"
+        #set $branch_snps_output = "input.tree.branch_snps.reconstruction.csv"
+        #set $svg_output = "input.tree.svg"
+        #set $png_output = "input.tree.png"
       #end if
 
-      ln -s '${sequences}' '${linked_input}' &&
+      ln -s '${sequences}' input.fasta &&
 
       squirrel
       #if $apobec3
@@ -50,7 +48,7 @@
       $no_iter_mask
 
       --threads \${GALAXY_SLOTS:-1}
-      '$linked_input' &&
+      input.fasta &&
 
       mv '${alignment_output}' '$alignment' &&
       mv '${tree_output}' '$tree'
@@ -140,7 +138,7 @@
       <data name="png" format="png" label="${tool.name} - phylotree png image"> 
         <filter>apobec3</filter>
       </data>
-      <data name="aa_recon" format="png" label="${tool.name} - amino acid mutations ancestral reconstruction">
+      <data name="aa_recon" format="png" label="${tool.name} - aa mutations ancestral reconstruction">
         <filter>apobec3</filter>
       </data>
       <data name="branch_snps" format="png" label="${tool.name} - apobec3 nt mutations">

diff --git a/tools/squirrel/squirrel-qc.xml b/tools/squirrel/squirrel-qc.xml
@@ -7,20 +7,18 @@
     <expand macro="version_command"/>
 
     <command detect_errors="exit_code"><![CDATA[
-      #set $input_file_name = str($sequences.element_identifier).replace(".fasta", "")
-      #set $linked_input = str($input_file_name) + '.fasta'
-      #set $mask_output = str($input_file_name) + '.suggested_mask.csv'
+      #set $mask_output = 'input.suggested_mask.csv'
       #set $exclude_output = 'suggested_to_exclude.csv'
 
-      ln -s '${sequences}' '${linked_input}' &&
+      ln -s '${sequences}' input.fasta &&
 
       squirrel
       --seq-qc
       --clade $clade
 
       --threads \${GALAXY_SLOTS:-Z}
 
-      '$linked_input' &&
+      input.fasta &&
 
       mv '${mask_output}' '$mask' &&
       mv '${exclude_output}' '$exclude'