diff QualityControl.xml @ 2:2f08fa7ab72c draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"

--- a/QualityControl.xml	Wed Sep 23 15:05:26 2020 +0000
+++ b/QualityControl.xml	Tue Oct 13 20:32:44 2020 +0000
@@ -26,7 +26,9 @@
   mkdir in_postFDR &&
   ${ ' '.join(["ln -s '%s' 'in_postFDR/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _]) }
 #end if
-mkdir out &&
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  mkdir out &&
+#end if
 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out_cm &&
 #end if
@@ -58,8 +60,10 @@
   -in_postFDR
   ${' '.join(["'in_postFDR/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])}
 #end if
--out
-'out/output.${gxy2omsext("mztab")}'
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  -out
+  'out/output.${gxy2omsext("mztab")}'
+#end if
 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   -out_cm
   'out_cm/output.${gxy2omsext("consensusxml")}'
@@ -81,7 +85,9 @@
 #end if
 
 ## Postprocessing
-&& mv 'out/output.${gxy2omsext("mztab")}' '$out'
+#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
+  && mv 'out/output.${gxy2omsext("mztab")}' '$out'
+#end if
 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
 #end if
@@ -111,22 +117,25 @@
       <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" optional="true" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/>
     </section>
     <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false">
-      <param name="force_no_fdr" argument="-MS2_id_rate:force_no_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run if FDR is missing (accepts all pep_ids as target hits)" help=""/>
+      <param name="assume_all_target" argument="-MS2_id_rate:assume_all_target" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits)" help=""/>
     </section>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
       <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
         <expand macro="list_string_san"/>
       </param>
     </expand>
-    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
-      <option value="out_cm_FLAG">out_cm (Forces the metric to run if FDR is missing (accepts all pep_ids as target hits))</option>
-      <option value="out_feat_FLAG">out_feat (Forces the metric to run if FDR is missing (accepts all pep_ids as target hits))</option>
+    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
+      <option value="out_FLAG">out (Output mzTab with QC information)</option>
+      <option value="out_cm_FLAG">out_cm (ConsensusXML with QC information (as metavalues))</option>
+      <option value="out_feat_FLAG">out_feat (FeatureXMLs with QC information (as metavalues))</option>
       <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
     </param>
   </inputs>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
+    <data name="out" label="${tool.name} on ${on_string}: out" format="mztab">
+      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
     <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
       <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
@@ -134,6 +143,9 @@
       <discover_datasets directory="out_feat" format="featurexml" pattern="__name__"/>
       <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
     </collection>
+    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
+      <filter>OPTIONAL_OUTPUTS is None</filter>
+    </data>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
@@ -145,6 +157,6 @@
   <help><![CDATA[Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.
 
 
-For more information, visit http://www.openms.de/documentation/TOPP_QualityControl.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_QualityControl.html]]></help>
   <expand macro="references"/>
 </tool>