Mercurial > repos > devteam > picard
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 |
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| date | Wed, 08 Feb 2017 12:45:35 -0500 |
| parents | 465cbb0cf2eb |
| children | 5053a18d9bc8 |
| 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
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1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>add comments to BAM dataset</description> |
| 3 <macros> | |
| 4 <import>picard_macros.xml</import> | |
| 5 </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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6 <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
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7 <command detect_errors="exit_code"><![CDATA[ |
| 5 | 8 @java_options@ |
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7e6fd3d0f16e
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
devteam
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9 @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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10 picard |
| 5 | 11 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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changeset
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12 INPUT='$escaped_element_identifier' |
| 5 | 13 OUTPUT="${outFile}" |
| 14 #for $element in $comments: | |
| 15 COMMENT="${element.comment}" | |
| 16 #end for | |
| 17 QUIET=true | |
| 18 VERBOSITY=ERROR | |
| 19 VALIDATION_STRINGENCY=${validation_stringency} | |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
9
diff
changeset
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20 ]]></command> |
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05087b27692a
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
devteam
parents:
9
diff
changeset
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21 |
| 5 | 22 <inputs> |
| 23 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> | |
| 24 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments"> | |
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5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
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changeset
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25 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> |
| 5 | 26 </repeat> |
| 27 | |
| 28 <expand macro="VS" /> | |
| 29 | |
| 30 </inputs> | |
| 31 | |
| 32 <outputs> | |
| 33 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/> | |
| 34 </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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35 |
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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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36 |
| 5 | 37 <tests> |
| 38 <test> | |
| 39 <param name="inputFile" value="picard_AddCommentsToBam.bam" /> | |
| 40 <param name="comment" value="test1" /> | |
| 41 <param name="validation_stringency" value="LENIENT" /> | |
| 42 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" /> | |
| 43 </test> | |
| 44 </tests> | |
| 45 <help> | |
| 46 | |
| 47 .. class:: infomark | |
| 48 | |
| 49 **Purpose** | |
| 50 | |
| 51 Adds one or more comments (@CO) to the header of a specified BAM dataset. | |
| 52 | |
| 53 @dataset_collections@ | |
| 54 | |
| 55 @description@ | |
| 56 | |
| 57 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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58 C=String Comments to add to the BAM file This option may be specified 0 or more times. |
| 5 | 59 |
| 60 @more_info@ | |
| 61 </help> | |
| 62 </tool> | |
| 63 | |
| 64 | |
| 65 | |
| 66 | |
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