# HG changeset patch
# User galaxyp
# Date 1516799338 18000
# Node ID acd0df26c1e969d061daa9027986200eebb2fb33
# Parent  e8f7be6a6e59438d29d07a6254c85fc17704977f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire commit 73496bb9686e60f25d1cccf3410f1c53bf92d5f5-dirty

diff -r e8f7be6a6e59 -r acd0df26c1e9 dia_umpire_se.xml
--- a/dia_umpire_se.xml	Tue Jan 23 14:45:50 2018 -0500
+++ b/dia_umpire_se.xml	Wed Jan 24 08:08:58 2018 -0500
@@ -22,17 +22,20 @@
 && echo " " >> $se_params 
 && echo "Thread = \$GALAXY_SLOTS" >> $se_params
 #if $input_prefix and len($input_prefix.strip()) > 0:
-#set $input_path = $ser_dir + "/" + $input_prefix.__str__ + "_rep" + str($i + 1) + ".mzXML" 
+#set $input_path = str($output_dir) + '/' + $input_prefix.__str__ + '_rep' + str($i + 1) + '.mzXML' 
 #else:
-#set $input_path = $ser_dir + "/" + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + ".mzXML"
+#set $input_path = str($output_dir) + '/' + $re.sub('\.[mM]\w+$','',$re.sub('[^-a-zA-Z0-9_.]','_',$input.name)) + '.mzXML'
 #end if
 && ln -s '${input}' '$input_path'
 &&  dia_umpire_se '$input_path' '$se_params'
 && cat $output_dir/*.log >> "$logfile"
 #if not $mgfs_as_collection:
-&& cp '$output_dir/*_Q1.mgf' '$q1_mgf'
-&& cp '$output_dir/*_Q2.mgf' '$q2_mgf'
-&& cp '$output_dir/*_Q3.mgf' '$q3_mgf'
+&& cp "$output_dir/"*_Q1.mgf '$q1_mgf'
+&& cp "$output_dir/"*_Q2.mgf '$q2_mgf'
+&& cp "$output_dir/"*_Q3.mgf '$q3_mgf'
+#end if
+#if $ExportPrecursorPeak:
+&& cp "$output_dir/"*PeakCluster.csv '$PrecursorPeak'
 #end if
 ]]>
     </command>
@@ -392,7 +395,7 @@
         <param name="ExportFragmentPeak" type="boolean" truevalue="true" falsevalue="false" checked="false" 
                label="ExportFragmentPeak"
                help="Output detailed information about detected MS2 signals"/>
-        <param name="se_extraction_data" type="boolean" truevalue="true" falsevalue="false" checked="false" 
+        <param name="se_extraction_data" type="boolean" truevalue="Signal Extraction data" falsevalue="diaumpire_se.params" checked="false" 
                label="Output Signal Extraction data for DIA_Umpire_Quant" />
         <param name="mgfs_as_collection" type="boolean" truevalue="true" falsevalue="false" checked="false" 
                label="Output MGFs as a collection" />
@@ -400,27 +403,28 @@
     </inputs>
 
     <outputs>
-        <data format="txt" name="logfile" label="${tool.name} log"/>
-        <data format="dia_umpire.ser" name="se_params" label="${tool.name} Signal Extraction data">
-            <filter>se_extraction_data</filter>
+        <data format="txt" name="logfile" label="${tool.name} ${on_string} log"/>
+        <data format="dia_umpire.ser" name="se_params" label="${tool.name} ${input.name} ${se_extraction_data}">
         </data>
-        <data format="csv" name="PrecursorPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv">
+        <data format="csv" name="PrecursorPeak" label="${tool.name} ${input.name} PeakCluster.csv" from_work_dir="gx_path/swath_PeakCurve.csv">
             <filter>ExportPrecursorPeak</filter>
         </data>
+        <!--
         <data format="csv" name="FragmentPeak" label="" from_work_dir="gx_path/swath_PeakCurve.csv">
             <filter>ExportFragmentPeak</filter>
         </data>
+        -->
         <collection name="dia_umpire_se_mgfs" type="list" label="${tool.name} MGFs">
             <filter>mgfs_as_collection</filter>
             <discover_datasets pattern="(?P&lt;name&gt;.*Q[1-3]\.mgf)" ext="mgf" visible="false" directory="gx_path" />
         </collection>
-        <data format="csv" name="q1_mgf" label="${tool.name} Q1.mgf" >
+        <data format="mgf" name="q1_mgf" label="${tool.name} ${input.name}_Q1.mgf" >
             <filter>not mgfs_as_collection</filter>
         </data>
-        <data format="csv" name="q2_mgf" label="${tool.name} Q2.mgf" >
+        <data format="mgf" name="q2_mgf" label="${tool.name} ${input.name}_Q2.mgf" >
             <filter>not mgfs_as_collection</filter>
         </data>
-        <data format="csv" name="q3_mgf" label="${tool.name} Q3.mgf" >
+        <data format="mgf" name="q3_mgf" label="${tool.name} ${input.name}_Q3.mgf" >
             <filter>not mgfs_as_collection</filter>
         </data>
     </outputs>