annotate picard_CleanSam.xml @ 9:5eaa8a968300 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
author devteam
date Fri, 09 Oct 2015 17:43:13 -0400
parents 3a3234d7a2e8
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 id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.0">
5
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
2 <description>perform SAM/BAM grooming</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 CleanSam
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 QUIET=true
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
14 VERBOSITY=ERROR
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
15 VALIDATION_STRINGENCY=${validation_stringency}
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
16 </command>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
17
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
18 <inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
19 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
20
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
21 <expand macro="VS" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
22
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
23 </inputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
24
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
25 <outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
26 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
27 </data>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
28 </outputs>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
29
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
30 <stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
31 <exit_code range="1:" level="fatal"/>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
32 </stdio>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
33
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
34 <tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
35 <test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
36 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
37 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" />
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
38 </test>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
39 </tests>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
40
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
41 <help>
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
42
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
43 .. class:: infomark
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
44
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
45 **Purpose**
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
46
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
47 Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
48
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
49 1. to soft-clip an alignment that hangs off the end of its reference sequence.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
50 2. to set MAPQ to 0 if a read is unmapped.
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
51
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
52 @dataset_collections@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
53
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
54 @more_info@
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
55
3d4f1fa26f0e Uploaded
devteam
parents:
diff changeset
56 </help>
8
3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
57 </tool>