Mercurial > repos > devteam > picard1106
comparison picard_FilterSamReads.xml @ 115:eaa932566ace draft
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author | devteam |
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date | Tue, 25 Feb 2014 16:37:52 -0500 |
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114:813fcb9201f1 | 115:eaa932566ace |
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1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="1.106.0"> | |
2 <description>Includes or excludes aligned reads or a list of reads from a BAM or SAM file</description> | |
3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements> | |
4 <command interpreter="bash"> | |
5 generic_outformat_wrapper.sh FilterSamReads $outFile $outputFormat | |
6 FILTER="${conditionfilter.Filter}" | |
7 INPUT=$input_file | |
8 #if $conditionfilter.Filter == "includeReadList" or $conditionfilter.Filter == "excludeReadList" : | |
9 #if str( $READ_LIST_FILE ): | |
10 READ_LIST_FILE="${READ_LIST_FILE}" | |
11 #end if | |
12 #end if | |
13 | |
14 #if str( $SORT_ORDER ): | |
15 SORT_ORDER="${SORT_ORDER}" | |
16 #end if | |
17 | |
18 | |
19 VALIDATION_STRINGENCY=LENIENT | |
20 QUIET=True | |
21 TMP_DIR="${__new_file_path__}" | |
22 </command> | |
23 | |
24 <stdio> | |
25 <exit_code range="0" level="warning" description="Tool finished correctly" /> | |
26 </stdio> | |
27 | |
28 <inputs> | |
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."/> | |
30 <conditional name="conditionfilter"> | |
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]}" | |
32 label="Filter"> | |
33 <option value="includeAligned" selected ="true">includeAligned</option> | |
34 <option value="excludeAligned">excludeAligned</option> | |
35 <option value="includeReadList">includeReadList</option> | |
36 <option value="excludeReadList">excludeReadList</option> | |
37 </param> | |
38 <when value="includeReadList"> | |
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="" /> | |
40 </when> | |
41 <when value="excludeReadList"> | |
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="" /> | |
43 </when> | |
44 </conditional> | |
45 | |
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" /> | |
47 | |
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." /> | |
49 | |
50 | |
51 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" /> | |
52 | |
53 </inputs> | |
54 | |
55 <outputs> | |
56 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: filtered ${outputFormat}"> | |
57 <change_format> | |
58 <when input="outputFormat" value="sam" format="sam" /> | |
59 </change_format> | |
60 </data> | |
61 </outputs> | |
62 | |
63 <help> | |
64 Picard documentation says: | |
65 | |
66 | |
67 FilterSamReads | |
68 | |
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. | |
70 | |
71 Option Description | |
72 INPUT=File The SAM or BAM file that will be filtered. Required. | |
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]} | |
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. | |
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} | |
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} | |
77 OUTPUT=File SAM or BAM file to write read excluded results to Required. | |
78 | |
79 | |
80 </help> | |
81 </tool> |