Mercurial > repos > devteam > picard1106
view picard_FilterSamReads.xml @ 150:896709401435 draft
dummy commit to attempt to merge multiple heads
author | Rayan Chikhi <chikhi@psu.edu> |
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date | Mon, 21 Jul 2014 16:28:40 -0400 |
parents | eaa932566ace |
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<tool name="FilterSamReads" id="picard_FilterSamReads" version="1.106.0"> <description>Includes or excludes aligned reads or a list of reads from a BAM or SAM file</description> <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> <command interpreter="bash"> generic_outformat_wrapper.sh FilterSamReads $outFile $outputFormat FILTER="${conditionfilter.Filter}" INPUT=$input_file #if $conditionfilter.Filter == "includeReadList" or $conditionfilter.Filter == "excludeReadList" : #if str( $READ_LIST_FILE ): READ_LIST_FILE="${READ_LIST_FILE}" #end if #end if #if str( $SORT_ORDER ): SORT_ORDER="${SORT_ORDER}" #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="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>