diff picard_CollectGcBiasMetrics.xml @ 7:08f69add4d06 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92

--- a/picard_CollectGcBiasMetrics.xml	Mon Nov 09 11:49:09 2015 -0500
+++ b/picard_CollectGcBiasMetrics.xml	Sun Nov 27 15:11:36 2016 -0500
@@ -4,21 +4,21 @@
     <import>picard_macros.xml</import>
   </macros>
   <expand macro="requirements">
-    <requirement type="package" version="3.1.2">R</requirement>
+    <requirement type="package" version="3.3.1">r</requirement>
   </expand>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     @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}" "${reference_fasta_filename}" &amp;&amp;
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
-    
-    java -jar \$JAVA_JAR_PATH/picard.jar
+
+    picard
     CollectGcBiasMetrics
     INPUT="${inputFile}"
     OUTPUT="${outFile}"
@@ -29,12 +29,12 @@
     IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
     REFERENCE_SEQUENCE="${reference_fasta_filename}"
     ASSUME_SORTED="${assume_sorted}"
-    
+
     VALIDATION_STRINGENCY="${validation_stringency}"
     QUIET=true
     VERBOSITY=ERROR
-  
-  </command>
+
+  ]]></command>
   <inputs>
     <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
     <conditional name="reference_source">
@@ -55,19 +55,19 @@
     </conditional>
     <param name="window_size" type="integer" value="100" label="The size of windows on the genome that are used to bin reads" help="WINDOW_SIZE; default=100"/>
     <param name="minimum_genome_fraction" type="float" value="0.00005" label="For summary metrics, exclude GC windows that include less than this fraction of the genome" help="MINIMUM_GENOME_FRACTION; default=0.0005"/>
-    <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> 
+    <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/>
     <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/>
-    
+
     <expand macro="VS" />
-    
+
   </inputs>
-  
+
   <outputs>
     <data format="tabular" name="summaryFile" label="${tool.name} on ${on_string}: Summary stats"/>
     <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/>
     <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/>
   </outputs>
-  
+
   <tests>
     <test>
       <param name="window_size" value="100" />
@@ -78,13 +78,10 @@
       <param name="ref_file" value="picard_CollectGcBiasMetrics_ref.fa" />
       <param name="inputFile" value="picard_CollectGcBiasMetrics.bam" ftype="bam" />
       <output name="outFile" file="picard_CollectGcBiasMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
-    </test> 
+    </test>
   </tests>
-  
-  <stdio>
-    <exit_code range="1:"  level="fatal"/>
-  </stdio>
-  
+
+
   <help>
 
 .. class:: infomark
@@ -97,15 +94,15 @@
 
 @description@
 
-  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value: 
-                                false. Possible values: {true, false} 
+  ALIGNED_READS_ONLY=Boolean    If set to true, calculate the base distribution over aligned reads only.  Default value:
+                                false. Possible values: {true, false}
 
-  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false. 
-                                This option can be set to 'null' to clear the default value. Possible values: {true, 
-                                false} 
+  PF_READS_ONLY=Boolean         If set to true calculate the base distribution over PF reads only.  Default value: false.
+                                This option can be set to 'null' to clear the default value. Possible values: {true,
+                                false}
 
   ASSUME_SORTED=Boolean
-  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default: True 
+  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default: True
 
 @more_info@