view picard_FilterSamReads.xml @ 131:3321bce585e5 draft

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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>