diff maxquant_mqpar.xml @ 21:8934bc76bb52 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 419e4f6608f60f0d73987b890d6b7f8854e874fb

--- a/maxquant_mqpar.xml	Tue Jan 31 18:14:40 2023 +0000
+++ b/maxquant_mqpar.xml	Mon Jun 19 17:02:17 2023 +0000
@@ -1,15 +1,5 @@
-<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="21.05">
+<tool id="maxquant_mqpar" name="MaxQuant (using mqpar.xml)" version="@VERSION@+galaxy@VERSION_SUFFIX_MQPAR@" profile="@PROFILE@">
     <macros>
-        <xml name="output" token_format="tabular" token_label="default description" token_name="default">
-            <data format="@FORMAT@" label="@LABEL@ for ${on_string}" name="@NAME@">
-                <filter>'@NAME@' in output</filter>
-            </data>
-        </xml>
-        <xml name="output_from_wdir" token_ext="txt" token_format="tabular" token_label="default description" token_name="default">
-            <data format="@FORMAT@" from_work_dir="combined/txt/@NAME@.@EXT@" label="@LABEL@ for ${on_string}" name="@NAME@">
-                <filter>'@NAME@' in output</filter>
-            </data>
-        </xml>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
@@ -50,7 +40,7 @@
         tar -zcf '$output_all' ./combined/txt
     #end if
   
-    #if $qc.do_it:
+    #if $qc.do_it == 'true':
         &&
         Rscript '$qr' '$qr_yaml'
         #if 'log' in $output:
@@ -148,7 +138,7 @@
             <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
             <param name="description_parse_rule" value="&gt;(.*)" />
             <param name="mqpar_input" value="mqpar/mqpar.xml" />
-            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
+            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
             <output name="evidence">
                 <assert_contents>
                     <has_text text="AEFVEVTK" />