changeset 10:777ccdd1d6e4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/picard_CollectAlignmentSummaryMetrics.xml	Fri Oct 09 17:43:13 2015 -0400
+++ b/picard_CollectAlignmentSummaryMetrics.xml	Sun Oct 11 10:46:17 2015 -0400
@@ -1,21 +1,24 @@
-<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.0">
+<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1">
   <description>writes a file containing summary alignment metrics</description>
   <macros>
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements" />
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
   <command>
     @java_options@
     ##set up input files
 
     #set $reference_fasta_filename = "localref.fa"
-    
+
     #if str( $reference_source.reference_source_selector ) == "history":
         ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
-    
+
     java -jar \$JAVA_JAR_PATH/picard.jar
     CollectAlignmentSummaryMetrics
     INPUT="${inputFile}"
@@ -24,11 +27,13 @@
     #for $sequence in $adapters:
         ADAPTER_SEQUENCE="${sequence.adapter}"
     #end for
-    METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"
+    #for $level in str($metric_accumulation_level).split(','):
+        METRIC_ACCUMULATION_LEVEL="${level}"
+    #end for
     IS_BISULFITE_SEQUENCED="${bisulphite}"
-    
+
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
-    
+
     ASSUME_SORTED="${assume_sorted}"
 
     VALIDATION_STRINGENCY="${validation_stringency}"
@@ -66,20 +71,12 @@
           <param name="adapter" type="text" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/>
     </repeat>
     <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" help="MAX_INSERT_SIZE"/>
-    
     <expand macro="VS" />
-    
+
   </inputs>
-  
   <outputs>
     <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/>
   </outputs>
-  
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
-  
   <tests>
     <test>
       <param name="bisulphite" value="false" />
@@ -92,7 +89,6 @@
       <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/>
     </test>
   </tests>
-  
   <help>
 
 .. class:: infomark