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1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="1.106.0">
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2 <description>Includes or excludes aligned reads or a list of reads from a BAM or SAM file</description>
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3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
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4 <command interpreter="bash">
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5 generic_outformat_wrapper.sh FilterSamReads $outFile $outputFormat
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6 FILTER="${conditionfilter.Filter}"
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7 INPUT=$input_file
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8 #if $conditionfilter.Filter == "includeReadList" or $conditionfilter.Filter == "excludeReadList" :
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9 #if str( $READ_LIST_FILE ):
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10 READ_LIST_FILE="${READ_LIST_FILE}"
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11 #end if
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12 #end if
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13
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14 #if str( $SORT_ORDER ):
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15 SORT_ORDER="${SORT_ORDER}"
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16 #end if
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17
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18
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19 VALIDATION_STRINGENCY=LENIENT
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20 QUIET=True
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21 TMP_DIR="${__new_file_path__}"
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22 </command>
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23
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24 <stdio>
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25 <exit_code range="0" level="warning" description="Tool finished correctly" />
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26 </stdio>
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27
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28 <inputs>
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29 <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."/>
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30 <conditional name="conditionfilter">
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31 <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]}"
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32 label="Filter">
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33 <option value="includeAligned" selected ="true">includeAligned</option>
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34 <option value="excludeAligned">excludeAligned</option>
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35 <option value="includeReadList">includeReadList</option>
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36 <option value="excludeReadList">excludeReadList</option>
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37 </param>
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38 <when value="includeReadList">
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39 <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="" />
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40 </when>
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41 <when value="excludeReadList">
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42 <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="" />
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43 </when>
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44 </conditional>
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45
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46 <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" />
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47
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48 <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." />
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49
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50
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51 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
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52
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53 </inputs>
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54
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55 <outputs>
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56 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: filtered ${outputFormat}">
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57 <change_format>
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58 <when input="outputFormat" value="sam" format="sam" />
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59 </change_format>
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60 </data>
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61 </outputs>
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62
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63 <help>
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64 Picard documentation says:
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65
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66
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67 FilterSamReads
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68
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69 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.
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70
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71 Option Description
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72 INPUT=File The SAM or BAM file that will be filtered. Required.
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73 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]}
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74 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.
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75 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}
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76 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}
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77 OUTPUT=File SAM or BAM file to write read excluded results to Required.
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78
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79
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80 </help>
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81 </tool>
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