diff picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml @ 5:3d4f1fa26f0e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml	Tue Dec 16 19:03:21 2014 -0500
@@ -0,0 +1,79 @@
+<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="1.126.0">
+  <description>revert the original base qualities and add the mate cigar tag</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
+    RevertOriginalBaseQualitiesAndAddMateCigar
+    
+    INPUT="${inputFile}"
+    OUTPUT="${outFile}"
+    
+    RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"
+    MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}"
+    
+    SORT_ORDER=coordinate
+    VALIDATION_STRINGENCY="${validation_stringency}"
+    QUIET=true
+    VERBOSITY=ERROR
+  
+  </command>
+  <inputs>
+    <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
+    <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>
+    <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/>
+
+    <expand macro="VS" />
+    
+  </inputs> 
+  
+  <outputs>
+    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/>
+  </outputs>
+  
+  <tests>
+    <test>
+      <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/>
+      <param name="restore_original_qualities" value="True"/>
+      <param name="max_records_to_examine" value="10000"/>
+      <param name="validation_stringency" value="LENIENT"/>
+      <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/>
+    </test>
+  </tests>
+  
+  <stdio>
+    <exit_code range="1:"  level="fatal"/>
+  </stdio>
+  
+  <help>
+
+**Purpose**
+
+Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs.
+
+@dataset_collections@
+
+@description@
+
+  RESTORE_ORIGINAL_QUALITIES=Boolean
+  OQ=Boolean                    True to restore original qualities from the OQ field to the QUAL field if available.  
+                                Default value: true. Possible values: {true, false} 
+  
+  MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not 
+                                output, given that there are a no original base qualities (if we are to restore) and mate 
+                                cigars exist. Set to 0 to never skip the file.  Default value: 10000.
+
+@more_info@
+
+  </help>
+</tool>
+
+