Mercurial > repos > devteam > picard
annotate picard_CleanSam.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 | 3a3234d7a2e8 |
| children | 05087b27692a |
| rev | line source |
|---|---|
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents:
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1 <tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>perform SAM/BAM grooming</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 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 | 7 <command> |
| 8 @java_options@ | |
| 9 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 10 CleanSam | |
| 11 INPUT="${inputFile}" | |
| 12 OUTPUT="${outFile}" | |
| 13 QUIET=true | |
| 14 VERBOSITY=ERROR | |
| 15 VALIDATION_STRINGENCY=${validation_stringency} | |
| 16 </command> | |
| 17 | |
| 18 <inputs> | |
| 19 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
| 20 | |
| 21 <expand macro="VS" /> | |
| 22 | |
| 23 </inputs> | |
| 24 | |
| 25 <outputs> | |
| 26 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset"> | |
| 27 </data> | |
| 28 </outputs> | |
| 29 | |
| 30 <stdio> | |
| 31 <exit_code range="1:" level="fatal"/> | |
| 32 </stdio> | |
| 33 | |
| 34 <tests> | |
| 35 <test> | |
| 36 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" /> | |
| 37 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" /> | |
| 38 </test> | |
| 39 </tests> | |
| 40 | |
| 41 <help> | |
| 42 | |
| 43 .. class:: infomark | |
| 44 | |
| 45 **Purpose** | |
| 46 | |
| 47 Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are: | |
| 48 | |
| 49 1. to soft-clip an alignment that hangs off the end of its reference sequence. | |
| 50 2. to set MAPQ to 0 if a read is unmapped. | |
| 51 | |
| 52 @dataset_collections@ | |
| 53 | |
| 54 @more_info@ | |
| 55 | |
| 56 </help> | |
|
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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> |