From d73eeec953810322205592edbbc68198cb0c9a26 Mon Sep 17 00:00:00 2001
From: Ammar Aziz <spidermine63@gmail.com>
Date: Wed, 15 Jan 2025 14:39:29 +1100
Subject: [PATCH] removed input oddities - READY?

---
 tools/squirrel/squirrel-phylo.xml | 20 +++++++++-----------
 tools/squirrel/squirrel-qc.xml    |  8 +++-----
 2 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/tools/squirrel/squirrel-phylo.xml b/tools/squirrel/squirrel-phylo.xml
index 39fff6257f2..182dc323ea0 100644
--- 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
index bae94bfd497..1af31510954 100644
--- a/tools/squirrel/squirrel-qc.xml
+++ b/tools/squirrel/squirrel-qc.xml
@@ -7,12 +7,10 @@
     <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
@@ -20,7 +18,7 @@
 
       --threads \${GALAXY_SLOTS:-Z}
 
-      '$linked_input' &&
+      input.fasta &&
 
       mv '${mask_output}' '$mask' &&
       mv '${exclude_output}' '$exclude'