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1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="1.106.0">
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2 <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>
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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 $output1 $outformat
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6 FILTER="${conditionfilter.Filter}"
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7 #if str( $READ_LIST_FILE ):
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8 READ_LIST_FILE="${READ_LIST_FILE}"
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9 #end if
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10 #if str( $SORT_ORDER ):
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11 SORT_ORDER="${SORT_ORDER}"
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12 #end if
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13 #if str( $WRITE_READS_FILES ):
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14 WRITE_READS_FILES="${WRITE_READS_FILES}"
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15 #end if
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16 #if str( $OUTPUT ):
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17 OUTPUT="${OUTPUT}"
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18 #end if
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19
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20 VALIDATION_STRINGENCY=LENIENT
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21 QUIET=True
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22 TMP_DIR="${__new_file_path__}"
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23 </command>
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24
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25 <stdio>
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26 <exit_code range="0" level="warning" description="Tool finished correctly" />
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27 </stdio>
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28
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29 <inputs>
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30 <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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31 <conditional name="conditionfilter">
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32 <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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33 label="Filter">
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34 <option value="includeAligned" selected ="true">includeAligned</option>
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35 <option value="excludeAligned">excludeAligned</option>
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36 <option value="includeReadList">includeReadList</option>
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37 <option value="excludeReadList">excludeReadList</option>
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38 </param>
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39 <when value="includeReadList">
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40 <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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41 </when>
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42 <when value="excludeReadList">
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43 <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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44 </when>
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45 </conditional>
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46 <param format="text" name="SORT_ORDER" type="string" label="SortOrder of the OUTPUT SAM or BAM file, otherwise use the SortOrder of the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}" help="" />
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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 <param name="WRITE_READS_FILES" type="boolean" checked="True" truevalue="true" falsevalue="false" label="Create .reads files (for debugging purposes)" help="" />
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51
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52 <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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53
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54 </inputs>
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55
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56 <outputs>
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57 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: filtered ${outputFormat}">
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58 <change_format>
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59 <when input="outputFormat" value="sam" format="sam" />
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60 </change_format>
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61 </data>
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62 </outputs>
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63
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64
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65
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66
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67 <tests>
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68 <!-- Here is a command line that works:
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69 java -jar ...
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70
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71 <param name="inputFile" value="XXCHANGEMEE-input" />
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72 <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
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73 </test> -->
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74 </tests>
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75 <help>
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76 Picard documentation says:
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77
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78
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79 FilterSamReads
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80
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81 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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82
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83 Option Description
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84 INPUT=File The SAM or BAM file that will be filtered. Required.
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85 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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86 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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87 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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88 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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89 OUTPUT=File SAM or BAM file to write read excluded results to Required.
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90
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91
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92 </help>
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93 </tool>
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