Mercurial > repos > devteam > picard

annotate picard_FilterSamReads.xml @ 17:fc288950c3b7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
author iuc
date Thu, 13 Apr 2017 19:09:24 -0400
parents 465cbb0cf2eb
children 5053a18d9bc8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
1 <tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.0">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>include or exclude aligned and unaligned reads and read lists</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
5 </macros>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
6 <expand macro="requirements" />
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
8 @java_options@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
9 @symlink_element_identifier@
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10 ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
11
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
12 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 SortSam
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
14 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 OUTPUT=query_sorted_bam.bam
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 SORT_ORDER=queryname
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 VALIDATION_STRINGENCY=LENIENT
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 VERBOSITY=ERROR
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
20
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
21 &&
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
22
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
23 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 FilterSamReads
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 INPUT=query_sorted_bam.bam
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 FILTER="${filter_type.filter}"
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
27
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ):
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 READ_LIST_FILE="${filter_type.read_list_file}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 #end if
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
31
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 SORT_ORDER=coordinate
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 VALIDATION_STRINGENCY="${validation_stringency}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 VERBOSITY=ERROR
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
37
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
38 ]]></command>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <inputs>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
40 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <conditional name="filter_type">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 <option value="includeAligned">Include aligned</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <option value="excludeAligned">Exclude aligned</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <option value="includeReadList">Include read list</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 <option value="excludeReadList">Exclude read list</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48 <when value="includeAligned"/> <!-- do nothing -->
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 <when value="excludeAligned"/> <!-- do nothing -->
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 <when value="includeReadList">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 <when value="excludeReadList">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 </when>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 </conditional>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
57
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58 <expand macro="VS" />
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
59
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
60 </inputs>
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
61
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 </outputs>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
65
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 <param name="filter" value="includeReadList"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 <param name="validation_stringency" value="LENIENT"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
72 <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76 <param name="filter" value="excludeReadList"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78 <param name="validation_stringency" value="LENIENT"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 8
diff changeset
79 <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
80 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
81 </tests>
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
82
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
83
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
85
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
86 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
87
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
88 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
89
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
90 ------
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
91
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
92 .. class:: warningmark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
93
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
94 **Warning on using this tool on BWA-MEM output**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
95
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
96 This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
97
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
98 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
99
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
100 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
101
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
102 FILTER=Filter Filter. Required. Possible values:
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
103 includeAligned [OUTPUT SAM/BAM will contain aligned
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
104 reads only. (Note that *both* first and
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
105 second of paired reads must be aligned to be included
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
106 in the OUTPUT SAM or BAM)],
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
107
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
108 excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only.
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
109 (Note that *both* first and second of pair must be aligned to be
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
110 excluded from the OUTPUT SAM or BAM)]
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
111
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
112 includeReadList [OUTPUT SAM/BAM will contain reads
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
113 that are supplied in the READ_LIST_FILE file]
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
114
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
115 excludeReadList [OUTPUT bam will contain
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
116 reads that are *not* supplied in the READ_LIST_FILE file]}
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
117
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
118 READ_LIST_FILE=File
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
119 RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
120 BAM file. Default value: null.
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
121
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
122 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
123
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
124 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
125 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
126
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
127