Mercurial > repos > devteam > picard
annotate picard_FixMateInformation.xml @ 8:3a3234d7a2e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
| author | devteam |
|---|---|
| date | Thu, 16 Jul 2015 15:53:10 -0400 |
| parents | 3d4f1fa26f0e |
| children | 05087b27692a |
| 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="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</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 | |
| 10 java -jar \$JAVA_JAR_PATH/picard.jar | |
| 11 FixMateInformation | |
| 12 INPUT="${inputFile}" | |
| 13 OUTPUT="${outFile}" | |
| 14 ASSUME_SORTED=${assume_sorted} | |
| 15 ADD_MATE_CIGAR=${add_mate_cigar} | |
| 16 | |
| 17 SORT_ORDER=coordinate | |
| 18 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 19 QUIET=true | |
| 20 VERBOSITY=ERROR | |
| 21 | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
| 25 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> | |
| 26 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/> | |
| 27 | |
| 28 <expand macro="VS" /> | |
| 29 | |
| 30 </inputs> | |
| 31 | |
| 32 <outputs> | |
| 33 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/> | |
| 34 </outputs> | |
| 35 | |
| 36 <tests> | |
| 37 <test> | |
| 38 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/> | |
| 39 <param name="add_mate_cigar" value="True"/> | |
| 40 <param name="assume_sorted" value="False"/> | |
| 41 <param name="validation_stringency" value="LENIENT"/> | |
| 42 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/> | |
| 43 </test> | |
| 44 </tests> | |
| 45 | |
| 46 <stdio> | |
| 47 <exit_code range="1:" level="fatal"/> | |
| 48 </stdio> | |
| 49 | |
| 50 <help> | |
| 51 | |
| 52 **Purpose** | |
| 53 | |
| 54 Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged. | |
| 55 | |
| 56 ------ | |
| 57 | |
| 58 .. class:: warningmark | |
| 59 | |
| 60 **Warning on using ASSUME_SORTED option** | |
| 61 | |
| 62 Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb | |
| 63 is to assume that the BAM you are working with is coordinate sorted. | |
| 64 | |
| 65 @dataset_collections@ | |
| 66 | |
| 67 @description@ | |
| 68 | |
| 69 ASSUME_SORTED=Boolean | |
| 70 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says | |
| 71 otherwise. Default value: false. | |
| 72 | |
| 73 ADD_MATE_CIGAR=Boolean | |
| 74 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true. | |
| 75 | |
| 76 @more_info@ | |
| 77 | |
| 78 </help> | |
| 79 </tool> | |
| 80 | |
| 81 |