diff picard_MergeSamFiles.xml @ 5:3d4f1fa26f0e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_MergeSamFiles.xml	Tue Dec 16 19:03:21 2014 -0500
@@ -0,0 +1,96 @@
+<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="1.126.0">
+  <description>merges multiple SAM/BAM datasets into one</description>
+  <requirements>
+    <requirement type="package" version="1.126.0">picard</requirement>
+  </requirements>
+  
+  <macros>
+    <import>picard_macros.xml</import>
+  </macros>
+  
+  <command>
+    @java_options@
+    
+    java -jar \$JAVA_JAR_PATH/picard.jar
+    MergeSamFiles
+    
+    #for $element in $inputFile:
+      INPUT="${element}"
+    #end for
+    
+    OUTPUT="${outFile}"
+    MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
+    
+    ASSUME_SORTED="${assume_sorted}"
+    #for $element in $comments:
+      COMMENT="${element.comment}"
+    #end for
+
+    USE_THREADING=true
+    SORT_ORDER=coordinate
+    VALIDATION_STRINGENCY="${validation_stringency}"
+    QUIET=true
+    VERBOSITY=ERROR
+  
+  </command>
+  <inputs>
+    <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+    <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
+    <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
+
+    <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
+      <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
+    </repeat>
+    
+    <expand macro="VS" />
+    
+  </inputs> 
+  
+  <outputs>
+    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
+      <param name="assume_sorted" value="False"/>
+      <param name="merge_sequence_dictionaries" value="False"/>
+      <param name="validation_stringency" value="LENIENT"/>
+      <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="2"/>
+    </test>
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+**Purpose**
+
+Merges multiple SAM/BAM datasets into one.
+
+@dataset_collections@
+
+@description@
+
+  ASSUME_SORTED=Boolean
+  AS=Boolean                    If true, assume that the input files are in the same sort order as the requested output 
+                                sort order, even if their headers say otherwise.  Default value: false. This option can 
+                                be set to 'null' to clear the default value. Possible values: {true, false} 
+  
+  MERGE_SEQUENCE_DICTIONARIES=Boolean
+  MSD=Boolean                   Merge the sequence dictionaries  Default value: false. This option can be set to 'null' 
+                                to clear the default value. Possible values: {true, false} 
+  
+  COMMENT=String
+  CO=String                     Comment(s) to include in the merged output file's header.  This option may be specified 0 
+                                or more times. 
+
+
+@more_info@
+
+  </help>
+</tool>
+
+