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changeset 10:2e297d531259 draft default tip

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planemo upload for repository https://unipept.ugent.be/apidocs commit 2f9f5541eeb65669ddb5ad74e8ba9fd437eea719
author galaxyp
date Fri, 25 Apr 2025 20:58:00 +0000
parents 21a560af5913
children
files unipept.py unipept.xml
diffstat 2 files changed, 39 insertions(+), 45 deletions(-) [+]
line wrap: on
line diff
--- a/unipept.py	Tue Mar 12 11:44:08 2024 +0000
+++ b/unipept.py	Fri Apr 25 20:58:00 2025 +0000
@@ -558,6 +558,8 @@
         post_data = []
         if options.equate_il:
             post_data.append(('equate_il', 'true'))
+        else:
+            post_data.append(('equate_il', 'false'))
         if options.names or options.json:
             post_data.append(('extra', 'true'))
             post_data.append(('names', 'true'))
--- a/unipept.xml	Tue Mar 12 11:44:08 2024 +0000
+++ b/unipept.xml	Fri Apr 25 20:58:00 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="unipept" name="Unipept" version="4.5.1" profile="22.05">
+<tool id="unipept" name="Unipept" version="6.2.4+galaxy0" profile="22.05">
     <description>retrieve taxonomy for peptides</description>
     <macros>
         <xml name="equate_il">
@@ -287,32 +287,27 @@
     <tests>
         <!-- Test-1 -->
         <test expect_num_outputs="2">
-            <param name="api" value="pept2lca"/>
-            <param name="fmt" value="tabular"/>
-            <param name="input_tsv" value="tryptic.tsv"/>
-            <param name="column" value="2"/>
-            <param name="extra" value="True"/>
-            <param name="names" value="True"/>
+            <param name="unipept|api" value="pept2lca"/>
+            <param name="peptide_src|fmt" value="tabular"/>
+            <param name="peptide_src|input_tsv" value="tryptic.tsv"/>
+            <param name="peptide_src|column" value="2"/>
+            <param name="unipept|extra" value="True"/>
+            <param name="unipept|names" value="True"/>
             <param name="selected_outputs" value="tsv,unmatched"/>
             <output name="output_tsv">
                 <assert_contents>
                     <has_text text="Homininae"/>
                 </assert_contents>
             </output>
-            <output name="output_unmatched">
-                <assert_contents>
-                    <has_text text="QTAMAV"/>
-                </assert_contents>
-            </output>
         </test>
         <!-- Test-2 -->
         <test expect_num_outputs="2">
-            <param name="api" value="pept2lca"/>
-            <param name="fmt" value="fasta"/>
-            <param name="input_fasta" value="peptide.fa"/>
-            <param name="equate_il" value="True"/>
-            <param name="extra" value="True"/>
-            <param name="names" value="True"/>
+            <param name="unipept|api" value="pept2lca"/>
+            <param name="peptide_src|fmt" value="fasta"/>
+            <param name="peptide_src|input_fasta" value="peptide.fa"/>
+            <param name="unipept|equate_il" value="True"/>
+            <param name="unipept|extra" value="True"/>
+            <param name="unipept|names" value="True"/>
             <param name="selected_outputs" value="json,tsv"/>
             <output name="output_json">
                 <assert_contents>
@@ -328,28 +323,27 @@
         </test>
         <!-- Test-3 -->
         <test expect_num_outputs="1">
-            <param name="api" value="pept2taxa"/>
-            <param name="fmt" value="fasta"/>
-            <param name="input_fasta" value="peptide.fa"/>
-            <param name="equate_il" value="True"/>
-            <param name="extra" value="False"/>
-            <param name="names" value="False"/>
+            <param name="unipept|api" value="pept2taxa"/>
+            <param name="peptide_src|fmt" value="fasta"/>
+            <param name="peptide_src|input_fasta" value="peptide.fa"/>
+            <param name="unipept|equate_il" value="True"/>
+            <param name="unipept|extra" value="False"/>
+            <param name="unipept|names" value="False"/>
             <param name="selected_outputs" value="tsv"/>
             <output name="output_tsv">
                 <assert_contents>
-                    <has_text text="sapiens"/>
-                    <has_text text="Cercocebus"/>
+                    <has_text text="Homo sapiens"/>
+                    <has_text text="Gorilla gorilla gorilla"/>
                 </assert_contents>
             </output>
         </test>
         <!-- Test-4 -->
         <test expect_num_outputs="5">
-            <param name="api" value="pept2funct"/>
-            <param name="fmt" value="tabular"/>
-            <param name="input_tsv" value="input.tsv"/>
-            <param name="column" value="2"/>
-            <param name="extra" value="True"/>
-            <param name="names" value="True"/>
+            <param name="unipept|api" value="pept2funct"/>
+            <param name="peptide_src|fmt" value="tabular"/>
+            <param name="peptide_src|input_tsv" value="input.tsv"/>
+            <param name="peptide_src|column" value="2"/>
+            <param name="unipept|extra" value="True"/>
             <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
             <output name="output_tsv">
                 <assert_contents>
@@ -376,12 +370,11 @@
         </test>
         <!-- Test-5 -->
         <test expect_num_outputs="5">
-            <param name="api" value="pept2funct"/>
-            <param name="fmt" value="tabular"/>
-            <param name="input_tsv" value="input.tsv"/>
-            <param name="column" value="2"/>
-            <param name="extra" value="True"/>
-            <param name="names" value="True"/>
+            <param name="unipept|api" value="pept2funct"/>
+            <param name="peptide_src|fmt" value="tabular"/>
+            <param name="peptide_src|input_tsv" value="input.tsv"/>
+            <param name="peptide_src|column" value="2"/>
+            <param name="unipept|extra" value="True"/>
             <param name="peptide_match" value="full"/>
             <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
             <output name="output_tsv">
@@ -410,12 +403,11 @@
         </test>
         <!-- Test-6 -->
         <test expect_num_outputs="5">
-            <param name="api" value="pept2funct"/>
-            <param name="fmt" value="tabular"/>
-            <param name="input_tsv" value="input.tsv"/>
-            <param name="column" value="2"/>
-            <param name="extra" value="True"/>
-            <param name="names" value="True"/>
+            <param name="unipept|api" value="pept2funct"/>
+            <param name="peptide_src|fmt" value="tabular"/>
+            <param name="peptide_src|input_tsv" value="input.tsv"/>
+            <param name="peptide_src|column" value="2"/>
+            <param name="unipept|extra" value="True"/>
             <param name="peptide_match" value="report"/>
             <param name="selected_outputs" value="tsv,ec_tsv,go_tsv,ipr_tsv,unmatched"/>
             <output name="output_tsv">
@@ -423,7 +415,7 @@
                     <has_text text="GO:0004802"/>
                     <has_text text="2.2.1.1"/>
                     <has_text text="IPR005475"/>
-                    <has_text_matching expression="AAEGGLSR\tAAEGGLSR\t6"/>
+                    <has_text_matching expression="AAEGGLSR\tAAEGGLSR\t111"/>
                 </assert_contents>
             </output>
             <output name="output_ec_tsv">