Mercurial > repos > devteam > picard1106

--- a/generic_outformat_wrapper.sh	Tue Feb 25 01:11:18 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#!/bin/bash
-eval java -Xmx2G -jar $JAVA_JAR_PATH/$1.jar O=$2.$3 ${*:4} 2>&1
-mv $2.$3 $2
--- a/picard_FilterSamReads.xml	Tue Feb 25 01:11:18 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-<tool name="FilterSamReads" id="picard_FilterSamReads" version="1.106.0">
-<description>Produces a new SAM or BAM file by including or excluding aligned reads or a list of reads names supplied in the READ_LIST_FILE from the INPUT SAM or BAM file.</description>
-<requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
-  <command interpreter="bash">
-        generic_outformat_wrapper.sh FilterSamReads $output1 $outformat
-          FILTER="${conditionfilter.Filter}"
-          #if str( $READ_LIST_FILE ):
-              READ_LIST_FILE="${READ_LIST_FILE}"
-          #end if
-          #if str( $SORT_ORDER ):
-              SORT_ORDER="${SORT_ORDER}"
-          #end if
-          #if str( $WRITE_READS_FILES ):
-              WRITE_READS_FILES="${WRITE_READS_FILES}"
-          #end if
-          #if str( $OUTPUT ):
-              OUTPUT="${OUTPUT}"
-          #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="bam,sam" name="input_file" type="data" label="SAM/BAM dataset that will be filterd" help="If empty, upload or import a SAM/BAM dataset."/>
-  		<conditional name="conditionfilter">
-  			<param name="Filter" type="select" help="Required. Possible values: {includeAligned [OUTPUT SAM/BAM will contain aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. (Note that *both* first and second of paired reads must be aligned to be included in the OUTPUT SAM or BAM)], excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only. INPUT SAM/BAM must be in queryname SortOrder. (Note that *both* first and second of pair must be aligned to be excluded from the OUTPUT SAM or BAM)], includeReadList [OUTPUT SAM/BAM will contain reads that are supplied in the READ_LIST_FILE file], excludeReadList [OUTPUT bam will contain reads that are *not* supplied in the READ_LIST_FILE file]}"
-         label="Filter">
-        		<option value="includeAligned" selected ="true">includeAligned</option>
-        		<option value="excludeAligned">excludeAligned</option>
-        		<option value="includeReadList">includeReadList</option>
-        		<option value="excludeReadList">excludeReadList</option>
-      	</param>
-      	<when value="includeReadList">
-      		<param format="data" name="READ_LIST_FILE" type="data" label="Read List File containing reads that will be included or excluded from the OUTPUT SAM or BAM file. Default value: null." help="" />
-      	</when>
-      	<when value="excludeReadList">
-      		<param format="data" name="READ_LIST_FILE" type="data" label="Read List File containing reads that will be included or excluded from the OUTPUT SAM or BAM file. Default value: null." help="" />
-      	</when>
-      </conditional>
-
-      <param name="SORT_ORDER" value="Sort order" type="text" label="SortOrder of the OUTPUT SAM or BAM file, otherwise use the SortOrder of the INPUT file. Default value: null." help="Possible values: {unsorted, queryname, coordinate}" size="100" />
-
- <param name="allowIncDictConcord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow incomplete dict concordance?" help="Allows a partial overlap of the BAM contigs with the new reference sequence contigs." />
-
-      <param name="WRITE_READS_FILES" type="boolean" checked="True" truevalue="true" falsevalue="false" label="Create .reads files (for debugging purposes)" help="" />
-
-       <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
-
-  </inputs>
-
-  <outputs>
-    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: filtered ${outputFormat}">
-      <change_format>
-        <when input="outputFormat" value="sam" format="sam" />
-      </change_format>
-    </data>
-  </outputs>
-
-  <help>
-Picard documentation says:
-
-
-FilterSamReads
-
-Produces a new SAM or BAM file by including or excluding aligned reads or a list of reads names supplied in the READ_LIST_FILE from the INPUT SAM or BAM file.
-
-Option	Description
-INPUT=File	The SAM or BAM file that will be filtered. Required.
-FILTER=Filter	Filter. Required. Possible values: {includeAligned [OUTPUT SAM/BAM will contain aligned reads only. INPUT SAM/BAM must be in queryname SortOrder. (Note that *both* first and second of paired reads must be aligned to be included in the OUTPUT SAM or BAM)], excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only. INPUT SAM/BAM must be in queryname SortOrder. (Note that *both* first and second of pair must be aligned to be excluded from the OUTPUT SAM or BAM)], includeReadList [OUTPUT SAM/BAM will contain reads that are supplied in the READ_LIST_FILE file], excludeReadList [OUTPUT bam will contain reads that are *not* supplied in the READ_LIST_FILE file]}
-READ_LIST_FILE=File	Read List File containing reads that will be included or excluded from the OUTPUT SAM or BAM file. Default value: null.
-SORT_ORDER=SortOrder	SortOrder of the OUTPUT SAM or BAM file, otherwise use the SortOrder of the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}
-WRITE_READS_FILES=Boolean	Create .reads files (for debugging purposes) Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
-OUTPUT=File	SAM or BAM file to write read excluded results to Required.
-
-
-  </help>
-</tool>