diff maxquant_mqpar.xml @ 4:9cb7dcc07dae draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 5e4f8567c0145de8c6f9344fe4ee4c3bf2a81e59"

--- a/maxquant_mqpar.xml	Sat Apr 11 11:50:09 2020 -0400
+++ b/maxquant_mqpar.xml	Fri Feb 19 21:25:06 2021 +0000
@@ -31,14 +31,14 @@
     --fasta_files='$fasta_files'
     --description_parse_rule='$description_parse_rule'
     --identifier_parse_rule='$identifier_parse_rule'
-    '$mqpar'
+    '$mqpar_input'
 
     &&
     maxquant mqpar.xml
     #if 'log' in $output:
         >> '$log'
     #end if
-    && mv '$mqpar' combined/txt/mqpar.xml
+    && mv mqpar.xml combined/txt/mqpar.xml
     #if 'output_all' in $output:
         &&
         tar -zcf '$output_all' ./combined/txt
@@ -102,7 +102,7 @@
                 </valid>
             </sanitizer>
         </param>
-        <param type="data" name="mqpar" format="xml"
+        <param type="data" name="mqpar_input" format="xml"
                label="mqpar.xml file with your search parameters. RAW file names 
                       must match the names displayed in galaxy. Their paths 
                       from the local machine are ignored. E.g. a file named
@@ -141,8 +141,8 @@
             <param name="fasta_files" value="bsa.fasta" />
             <param name="identifier_parse_rule" value="&gt;([^\s]*)" />
             <param name="description_parse_rule" value="&gt;(.*)" />
-            <param name="mqpar" value="mqpar.xml" />
-            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,output_all" />
+            <param name="mqpar_input" value="mqpar.xml" />
+            <param name="output" value="evidence,msms,mzTab,allPeptides,msmsScans,mzRange,parameters,peptides,peptideSection,proteinGroups,summary,modificationSpecificPeptides,mqpar,output_all" />
             <output name="evidence" file="txt/evidence.txt" />
             <output name="msms" file="txt/msms.txt" lines_diff="2" />
             <output name="allPeptides" file="txt/allPeptides.txt" lines_diff="32" />
@@ -153,6 +153,7 @@
             <output name="proteinGroups" file="txt/proteinGroups.txt" />
             <output name="summary" file="txt/summary.txt" />
             <output name="modificationSpecificPeptides" file="txt/modificationSpecificPeptides.txt" />
+            <output name="mqpar" file="txt/mqpar.xml" lines_diff="8" />
         </test>
     </tests>
     <help><![CDATA[