Mercurial > repos > devteam > picard
diff picard_FilterSamReads.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 | 41b8d087a2d2 |
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--- a/picard_FilterSamReads.xml Sun Nov 27 15:11:36 2016 -0500 +++ b/picard_FilterSamReads.xml Tue Dec 06 10:04:26 2016 -0500 @@ -6,35 +6,35 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @java_options@ - + @symlink_element_identifier@ ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order - + picard SortSam - INPUT="${inputFile}" + INPUT='$inputFile.element_identifier' OUTPUT=query_sorted_bam.bam SORT_ORDER=queryname VALIDATION_STRINGENCY=LENIENT QUIET=true VERBOSITY=ERROR - + && - + picard FilterSamReads INPUT=query_sorted_bam.bam FILTER="${filter_type.filter}" - + #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ): READ_LIST_FILE="${filter_type.read_list_file}" #end if - + OUTPUT="${outFile}" SORT_ORDER=coordinate VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - + ]]></command> <inputs> <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> @@ -54,15 +54,15 @@ <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/> </when> </conditional> - + <expand macro="VS" /> - - </inputs> - + + </inputs> + <outputs> <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/> </outputs> - + <tests> <test> <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> @@ -79,8 +79,8 @@ <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/> </test> </tests> - - + + <help> **Purpose** @@ -93,32 +93,32 @@ **Warning on using this tool on BWA-MEM output** -This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts. +This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts. @dataset_collections@ @description@ FILTER=Filter Filter. Required. Possible values: - includeAligned [OUTPUT SAM/BAM will contain aligned - reads only. (Note that *both* first and + includeAligned [OUTPUT SAM/BAM will contain aligned + reads only. (Note that *both* first and second of paired reads must be aligned to be included - in the OUTPUT SAM or BAM)], - + in the OUTPUT SAM or BAM)], + excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only. - (Note that *both* first and second of pair must be aligned to be + (Note that *both* first and second of pair must be aligned to be excluded from the OUTPUT SAM or BAM)] - - includeReadList [OUTPUT SAM/BAM will contain reads + + includeReadList [OUTPUT SAM/BAM will contain reads that are supplied in the READ_LIST_FILE file] - - excludeReadList [OUTPUT bam will contain - reads that are *not* supplied in the READ_LIST_FILE file]} + + excludeReadList [OUTPUT bam will contain + reads that are *not* supplied in the READ_LIST_FILE file]} READ_LIST_FILE=File - RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or - BAM file. Default value: null. - + RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or + BAM file. Default value: null. + @more_info@ </help>