113
|
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
|
|
47 <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" />
|
|
48
|
|
49 <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." />
|
|
50
|
|
51 <param name="WRITE_READS_FILES" type="boolean" checked="True" truevalue="true" falsevalue="false" label="Create .reads files (for debugging purposes)" help="" />
|
|
52
|
|
53 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
|
|
54
|
|
55 </inputs>
|
|
56
|
|
57 <outputs>
|
|
58 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: filtered ${outputFormat}">
|
|
59 <change_format>
|
|
60 <when input="outputFormat" value="sam" format="sam" />
|
|
61 </change_format>
|
|
62 </data>
|
|
63 </outputs>
|
|
64
|
|
65 <help>
|
|
66 Picard documentation says:
|
|
67
|
|
68
|
|
69 FilterSamReads
|
|
70
|
|
71 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.
|
|
72
|
|
73 Option Description
|
|
74 INPUT=File The SAM or BAM file that will be filtered. Required.
|
|
75 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]}
|
|
76 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.
|
|
77 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}
|
|
78 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}
|
|
79 OUTPUT=File SAM or BAM file to write read excluded results to Required.
|
|
80
|
|
81
|
|
82 </help>
|
|
83 </tool>
|