diff OpenSwathFileSplitter.xml @ 10:2d856cba192b draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e"

--- a/OpenSwathFileSplitter.xml	Wed Sep 09 19:55:24 2020 +0000
+++ b/OpenSwathFileSplitter.xml	Thu Sep 24 12:17:48 2020 +0000
@@ -18,7 +18,7 @@
 ## Preprocessing
 mkdir in &&
 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir adv_opts_cond.outputDirectory &&
+mkdir outputDirectory &&
 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_qc &&
 #end if
@@ -32,7 +32,7 @@
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
 -outputDirectory
-adv_opts_cond.outputDirectory/
+outputDirectory/
 #if "out_qc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out_qc
   'out_qc/output.${gxy2omsext("json")}'
@@ -66,8 +66,8 @@
     </param>
   </inputs>
   <outputs>
-    <collection type="list" name="adv_opts_cond.outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
-      <discover_datasets directory="adv_opts_cond.outputDirectory" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+    <collection type="list" name="outputDirectory" label="${tool.name} on ${on_string}: outputDirectory">
+      <discover_datasets directory="outputDirectory" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
     </collection>
     <data name="out_qc" label="${tool.name} on ${on_string}: out_qc" format="json">
       <filter>OPTIONAL_OUTPUTS is not None and "out_qc_FLAG" in OPTIONAL_OUTPUTS</filter>