comparison picard_FilterSamReads.xml @ 107:5b10a8aea040 draft

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author devteam
date Tue, 25 Feb 2014 00:45:51 -0500
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106:6c17c441f8cd 107:5b10a8aea040
1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="1.106.0">
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>
3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
4 <command interpreter="bash">
5 generic_outformat_wrapper.sh FilterSamReads $output1 $outformat
6 FILTER="${conditionfilter.Filter}"
7 #if str( $READ_LIST_FILE ):
8 READ_LIST_FILE="${READ_LIST_FILE}"
9 #end if
10 #if str( $SORT_ORDER ):
11 SORT_ORDER="${SORT_ORDER}"
12 #end if
13 #if str( $WRITE_READS_FILES ):
14 WRITE_READS_FILES="${WRITE_READS_FILES}"
15 #end if
16 #if str( $OUTPUT ):
17 OUTPUT="${OUTPUT}"
18 #end if
19
20 VALIDATION_STRINGENCY=LENIENT
21 QUIET=True
22 TMP_DIR="${__new_file_path__}"
23 </command>
24
25 <stdio>
26 <exit_code range="0" level="warning" description="Tool finished correctly" />
27 </stdio>
28
29 <inputs>
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."/>
31 <conditional name="conditionfilter">
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]}"
33 label="Filter">
34 <option value="includeAligned" selected ="true">includeAligned</option>
35 <option value="excludeAligned">excludeAligned</option>
36 <option value="includeReadList">includeReadList</option>
37 <option value="excludeReadList">excludeReadList</option>
38 </param>
39 <when value="includeReadList">
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="" />
41 </when>
42 <when value="excludeReadList">
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="" />
44 </when>
45 </conditional>
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="" />
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 <param name="WRITE_READS_FILES" type="boolean" checked="True" truevalue="true" falsevalue="false" label="Create .reads files (for debugging purposes)" help="" />
51
52 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
53
54 </inputs>
55
56 <outputs>
57 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: filtered ${outputFormat}">
58 <change_format>
59 <when input="outputFormat" value="sam" format="sam" />
60 </change_format>
61 </data>
62 </outputs>
63
64
65
66
67 <tests>
68 <!-- Here is a command line that works:
69 java -jar ...
70
71 <param name="inputFile" value="XXCHANGEMEE-input" />
72 <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
73 </test> -->
74 </tests>
75 <help>
76 Picard documentation says:
77
78
79 FilterSamReads
80
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.
82
83 Option Description
84 INPUT=File The SAM or BAM file that will be filtered. Required.
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]}
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.
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}
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}
89 OUTPUT=File SAM or BAM file to write read excluded results to Required.
90
91
92 </help>
93 </tool>