Mercurial > repos > devteam > picard
annotate picard_MergeSamFiles.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 | 5eaa8a968300 |
| 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:
5
diff
changeset
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1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0"> |
| 5 | 2 <description>merges multiple SAM/BAM datasets into one</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 MergeSamFiles | |
| 12 | |
| 13 #for $element in $inputFile: | |
| 14 INPUT="${element}" | |
| 15 #end for | |
| 16 | |
| 17 OUTPUT="${outFile}" | |
| 18 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}" | |
| 19 | |
| 20 ASSUME_SORTED="${assume_sorted}" | |
| 21 #for $element in $comments: | |
| 22 COMMENT="${element.comment}" | |
| 23 #end for | |
| 24 | |
| 25 USE_THREADING=true | |
| 26 SORT_ORDER=coordinate | |
| 27 VALIDATION_STRINGENCY="${validation_stringency}" | |
| 28 QUIET=true | |
| 29 VERBOSITY=ERROR | |
| 30 | |
| 31 </command> | |
| 32 <inputs> | |
| 33 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
| 34 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/> | |
| 35 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/> | |
| 36 | |
| 37 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments"> | |
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9
5eaa8a968300
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 1869970193a1878acbc0f8a79b81dd02b37f1dc1
devteam
parents:
8
diff
changeset
|
38 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> |
| 5 | 39 </repeat> |
| 40 | |
| 41 <expand macro="VS" /> | |
| 42 | |
| 43 </inputs> | |
| 44 | |
| 45 <outputs> | |
| 46 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/> | |
| 47 </outputs> | |
| 48 | |
| 49 <tests> | |
| 50 <test> | |
| 51 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/> | |
| 52 <param name="assume_sorted" value="False"/> | |
| 53 <param name="merge_sequence_dictionaries" value="False"/> | |
| 54 <param name="validation_stringency" value="LENIENT"/> | |
| 55 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="2"/> | |
| 56 </test> | |
| 57 </tests> | |
| 58 | |
| 59 <stdio> | |
| 60 <exit_code range="1:" level="fatal"/> | |
| 61 </stdio> | |
| 62 | |
| 63 <help> | |
| 64 | |
| 65 **Purpose** | |
| 66 | |
| 67 Merges multiple SAM/BAM datasets into one. | |
| 68 | |
| 69 @dataset_collections@ | |
| 70 | |
| 71 @description@ | |
| 72 | |
| 73 ASSUME_SORTED=Boolean | |
| 74 AS=Boolean If true, assume that the input files are in the same sort order as the requested output | |
| 75 sort order, even if their headers say otherwise. Default value: false. This option can | |
| 76 be set to 'null' to clear the default value. Possible values: {true, false} | |
| 77 | |
| 78 MERGE_SEQUENCE_DICTIONARIES=Boolean | |
| 79 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null' | |
| 80 to clear the default value. Possible values: {true, false} | |
| 81 | |
| 82 COMMENT=String | |
| 83 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0 | |
| 84 or more times. | |
| 85 | |
| 86 | |
| 87 @more_info@ | |
| 88 | |
| 89 </help> | |
| 90 </tool> | |
| 91 | |
| 92 |