Mercurial > repos > devteam > picard

annotate picard_SortSam.xml @ 32:f9242e01365a 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 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents 2a17c789e0a5
children 3f254c5ced1d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
1 <tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>sort SAM/BAM dataset</description>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
3 <macros>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
4 <import>picard_macros.xml</import>
20
2a17c789e0a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents: 19
diff changeset
5 <token name="@WRAPPER_VERSION@">1</token>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
6 </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
7 <expand macro="requirements" />
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
9 #if $sort_order == "queryname":
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
10 #set $output = "output.sam"
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
11 ln -s '${outFile}' output.sam &&
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
12 #else:
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
13 #set $output = $outFile
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
14 #end if
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 @java_options@
13
7e6fd3d0f16e planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents: 12
diff changeset
16 @symlink_element_identifier@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
17 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 SortSam
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
19 INPUT='$escaped_element_identifier'
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
20 OUTPUT='${output}'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 SORT_ORDER="${sort_order}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 VALIDATION_STRINGENCY=${validation_stringency}
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
25 ]]></command>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
26
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 <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"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
29 <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate. Selecting Queryname will output SAM file, as Galaxy does not support BAM files that are not coordinate sorted.">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 <option value="coordinate" selected="True">Coordinate</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 <option value="queryname">Queryname</option>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 </param>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 </inputs>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
35
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 <outputs>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
37 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Alignment sorted in ${sort_order} order">
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
38 <change_format>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
39 <when input="sort_order" value="queryname" format="sam"/>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
40 </change_format>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 </data>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 </outputs>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
43
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
44
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <tests>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
46 <!-- This test fails when setting metadata on non-coordinate sorted bam files.
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
47 This should be handled better in Galaxy (info as of release 16.0).
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
48 Workaroudn is to produce queryname sorted sam files.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 <param name="sort_order" value="queryname"/>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
52 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
53 </test>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
54 -->
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
55 <test>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
56 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
57 <param name="sort_order" value="queryname"/>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
58 <output name="outFile" file="picard_SortSam_test1.sam" ftype="sam" lines_diff="4" compare="contains"/>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
59 </test>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
60 <test>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
61 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
62 <param name="sort_order" value="coordinate"/>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
63 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="4"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65 </tests>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
66
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73 Sorts the input SAM or BAM.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
78
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
79 SORT_ORDER=SortOrder
11
efc56ee1ade4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 8
diff changeset
80 SO=SortOrder Sort order of output file. You can either sort by queryname or by coordinate.
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 11
diff changeset
81
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
82 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
83
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
84 </help>
19
5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents: 14
diff changeset
85 <expand macro="citations" />
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
86 </tool>