# HG changeset patch
# User devteam
# Date 1393372509 18000
# Node ID 21bf2afb895ca428d0f996307cf93d1dfc87fe4a
# Parent  5fe20cda6a51012c98226ed680f51c7de43fe3cf
Uploaded

diff -r 5fe20cda6a51 -r 21bf2afb895c picard_MeanQualityByCylce.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/picard_MeanQualityByCylce.xml	Tue Feb 25 18:55:09 2014 -0500
@@ -0,0 +1,88 @@
+<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.106.0">
+<description>Calculates mean quality</description>
+<requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
+  <command interpreter="bash">
+  	<!--	generic_outformat_wrapper.sh MeanQualityByCycle $outFile $outputFormat
+ 			CHART_OUTPUT=File	A file (with .pdf extension) to write the chart to. Required. 
+ 
+          #if str( $ALIGNED_READS_ONLY ):
+              ALIGNED_READS_ONLY="${ALIGNED_READS_ONLY}"
+          #end if
+          #if str( $PF_READS_ONLY ):
+              PF_READS_ONLY="${PF_READS_ONLY}"
+          #end if
+          #if str( $INPUT ):
+              INPUT="${INPUT}"
+          #end if
+          #if str( $OUTPUT ):
+              OUTPUT="${OUTPUT}"
+          #end if
+          #if str( $REFERENCE_SEQUENCE ):
+              REFERENCE_SEQUENCE="${REFERENCE_SEQUENCE}"
+          #end if
+          #if str( $ASSUME_SORTED ):
+              ASSUME_SORTED="${ASSUME_SORTED}"
+          #end if
+          #if str( $STOP_AFTER ):
+              STOP_AFTER="${STOP_AFTER}"
+          #end if
+ 
+      VALIDATION_STRINGENCY=LENIENT
+      QUIET=True
+      TMP_DIR="${__new_file_path__}" -->
+  </command>
+   
+  <stdio>
+    <exit_code range="0" level="warning" description="Tool finished correctly" />
+  </stdio>
+   
+  <inputs>
+   <!--
+      <param format="XXCHANGEMEEE" name="ALIGNED_READS_ONLY" type="boolean" label="If set to true, calculate mean quality over aligned reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
+      <param format="XXCHANGEMEEE" name="PF_READS_ONLY" type="boolean" label="If set to true calculate mean quality over PF reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
+      <param format="XXCHANGEMEEE" name="INPUT" type="data" label="Input SAM or BAM file. Required." help="" />
+      <param format="XXCHANGEMEEE" name="OUTPUT" type="data" label="File to write the output to. Required." help="" />
+      <param format="XXCHANGEMEEE" name="REFERENCE_SEQUENCE" type="data" label="Reference sequence fasta Default value: null." help="" />
+      <param format="XXCHANGEMEEE" name="ASSUME_SORTED" type="boolean" label="If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
+      <param format="XXCHANGEMEEE" name="STOP_AFTER" type="string" label="Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value." help="" />
+  -->
+  </inputs>
+  <outputs>
+  <!--
+    <data name="outFile" format="XXCHANGEMEEE">
+  
+    </data>
+      -->
+  </outputs>
+  <tests>
+  <test>
+     <!-- Here is a command line that works:
+        java -jar ...
+     -->
+     <!--
+      <param name="inputFile" value="XXCHANGEMEE-input" />
+      <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
+        -->
+    </test>
+  </tests>
+  <help>
+Picard documentation says:
+ 
+  
+MeanQualityByCycle
+
+Usage: program [options...]
+
+Option	Description
+CHART_OUTPUT=File	A file (with .pdf extension) to write the chart to. Required.
+ALIGNED_READS_ONLY=Boolean	If set to true, calculate mean quality over aligned 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 mean quality over PF reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
+INPUT=File	Input SAM or BAM file. Required.
+OUTPUT=File	File to write the output to. Required.
+REFERENCE_SEQUENCE=File	Reference sequence fasta Default value: null.
+ASSUME_SORTED=Boolean	If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
+STOP_AFTER=Long	Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value. 
+
+ 
+  </help>
+</tool>