Mercurial > repos > devteam > picard
diff picard_MergeSamFiles.xml @ 8:e417b1d6288d draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author | devteam |
---|---|
date | Tue, 06 Dec 2016 10:04:26 -0500 |
parents | 08f69add4d06 |
children | 486d7500da69 |
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--- a/picard_MergeSamFiles.xml Sun Nov 27 15:11:36 2016 -0500 +++ b/picard_MergeSamFiles.xml Tue Dec 06 10:04:26 2016 -0500 @@ -6,17 +6,16 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @java_options@ - picard MergeSamFiles - + #for $element in $inputFile: INPUT="${element}" #end for - + OUTPUT="${outFile}" MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}" - + ASSUME_SORTED="${assume_sorted}" #for $element in $comments: COMMENT="${element.comment}" @@ -27,7 +26,7 @@ VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - + ]]></command> <inputs> <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> @@ -37,15 +36,15 @@ <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments"> <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> </repeat> - + <expand macro="VS" /> - - </inputs> - + + </inputs> + <outputs> <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/> </outputs> - + <tests> <test> <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/> @@ -55,8 +54,8 @@ <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="4"/> </test> </tests> - - + + <help> **Purpose** @@ -68,17 +67,17 @@ @description@ ASSUME_SORTED=Boolean - AS=Boolean If true, assume that the input files are in the same sort order as the requested output - sort order, even if their headers say otherwise. Default value: false. This option can - be set to 'null' to clear the default value. Possible values: {true, false} - + AS=Boolean If true, assume that the input files are in the same sort order as the requested output + sort order, even if their headers say otherwise. Default value: false. This option can + be set to 'null' to clear the default value. Possible values: {true, false} + MERGE_SEQUENCE_DICTIONARIES=Boolean - MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null' - to clear the default value. Possible values: {true, false} - + MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null' + to clear the default value. Possible values: {true, false} + COMMENT=String - CO=String Comment(s) to include in the merged output file's header. This option may be specified 0 - or more times. + CO=String Comment(s) to include in the merged output file's header. This option may be specified 0 + or more times. @more_info@