annotate picard_AddCommentsToBam.xml @ 16:6741a8ace658 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:45:35 -0500
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="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.0">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>add comments to BAM dataset</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: 9
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@
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
10 picard
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 AddCommentsToBam
14
465cbb0cf2eb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
parents: 13
diff changeset
12 INPUT='$escaped_element_identifier'
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 #for $element in $comments:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 COMMENT="${element.comment}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 #end for
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 VALIDATION_STRINGENCY=${validation_stringency}
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
20 ]]></command>
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
21
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
25 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 </repeat>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 </outputs>
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
35
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
36
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <param name="comment" value="test1" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <param name="validation_stringency" value="LENIENT" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 Adds one or more comments (@CO) to the header of a specified BAM dataset.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 COMMENT=String
12
05087b27692a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents: 9
diff changeset
58 C=String Comments to add to the BAM file This option may be specified 0 or more times.
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 </tool>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
65
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
66
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
67
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
68
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
69
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
70
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
71
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
72
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
73
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
74
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
75