Mercurial > repos > devteam > picard
annotate picard_AddCommentsToBam.xml @ 21:6f9c0884a3e7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661
| author | iuc |
|---|---|
| date | Tue, 16 Oct 2018 11:49:10 -0400 |
| parents | 2a17c789e0a5 |
| children | f9242e01365a |
| rev | line source |
|---|---|
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
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1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> |
| 5 | 2 <description>add comments to BAM dataset</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
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2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
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5 <token name="@WRAPPER_VERSION@">1</token> |
| 5 | 6 </macros> |
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3a3234d7a2e8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
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7 <expand macro="requirements" /> |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
| 5 | 9 @java_options@ |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
parents:
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changeset
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10 @symlink_element_identifier@ |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
9
diff
changeset
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11 picard |
| 5 | 12 AddCommentsToBam |
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465cbb0cf2eb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f
devteam
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13 INPUT='$escaped_element_identifier' |
| 5 | 14 OUTPUT="${outFile}" |
| 15 #for $element in $comments: | |
| 16 COMMENT="${element.comment}" | |
| 17 #end for | |
| 18 QUIET=true | |
| 19 VERBOSITY=ERROR | |
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2a17c789e0a5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
iuc
parents:
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changeset
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20 @TMPDIR_OPTION@ |
| 5 | 21 VALIDATION_STRINGENCY=${validation_stringency} |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
9
diff
changeset
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22 ]]></command> |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
9
diff
changeset
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23 |
| 5 | 24 <inputs> |
| 25 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> | |
| 26 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments"> | |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
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27 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> |
| 5 | 28 </repeat> |
| 29 | |
| 30 <expand macro="VS" /> | |
| 31 | |
| 32 </inputs> | |
| 33 | |
| 34 <outputs> | |
| 35 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/> | |
| 36 </outputs> | |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
9
diff
changeset
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37 |
|
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
9
diff
changeset
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38 |
| 5 | 39 <tests> |
| 40 <test> | |
| 41 <param name="inputFile" value="picard_AddCommentsToBam.bam" /> | |
| 42 <param name="comment" value="test1" /> | |
| 43 <param name="validation_stringency" value="LENIENT" /> | |
| 44 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" /> | |
| 45 </test> | |
| 46 </tests> | |
| 47 <help> | |
| 48 | |
| 49 .. class:: infomark | |
| 50 | |
| 51 **Purpose** | |
| 52 | |
| 53 Adds one or more comments (@CO) to the header of a specified BAM dataset. | |
| 54 | |
| 55 @dataset_collections@ | |
| 56 | |
| 57 @description@ | |
| 58 | |
| 59 COMMENT=String | |
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12
05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
9
diff
changeset
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60 C=String Comments to add to the BAM file This option may be specified 0 or more times. |
| 5 | 61 |
| 62 @more_info@ | |
| 63 </help> | |
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5053a18d9bc8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
iuc
parents:
14
diff
changeset
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64 <expand macro="citations" /> |
| 5 | 65 </tool> |