annotate picard_AddCommentsToBam.xml @ 11:efc56ee1ade4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:23:17 -0500
parents 5eaa8a968300
children 05087b27692a
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" />
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
7 <command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
8 @java_options@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
9 java -jar \$JAVA_JAR_PATH/picard.jar
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
10 AddCommentsToBam
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
11 INPUT="${inputFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
12 OUTPUT="${outFile}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
13 #for $element in $comments:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 COMMENT="${element.comment}"
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 #end for
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 VALIDATION_STRINGENCY=${validation_stringency}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 </command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
9
5eaa8a968300 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents: 8
diff changeset
24 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 </repeat>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 <stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 <exit_code range="1:" level="fatal"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 </stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42 <param name="comment" value="test1" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 <param name="validation_stringency" value="LENIENT" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53 Adds one or more comments (@CO) to the header of a specified BAM dataset.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
57 @description@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
58
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
59 COMMENT=String
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
60 C=String Comments to add to the BAM file This option may be specified 0 or more times.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
61
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
62 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
63 </help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
64 </tool>
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
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
76
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
77