Mercurial > repos > devteam > picard
view picard_FilterSamReads.xml @ 19:862298bf72d7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9c268f08be6d363990a822fc941e031dd13be3f4
author | iuc |
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date | Fri, 31 May 2019 03:21:17 -0400 |
parents | a5a13ea16d17 |
children | c943f4a04af0 |
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<tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> <description>include or exclude aligned and unaligned reads and read lists</description> <macros> <import>picard_macros.xml</import> <token name="@WRAPPER_VERSION@">1</token> </macros> <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='$escaped_element_identifier' OUTPUT=query_sorted_bam.bam SORT_ORDER=queryname VALIDATION_STRINGENCY=LENIENT QUIET=true VERBOSITY=ERROR @TMPDIR_OPTION@ && picard FilterSamReads INPUT=query_sorted_bam.bam FILTER="${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 @TMPDIR_OPTION@ ]]></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"/> <conditional name="filter_type"> <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> <option value="includeAligned">Include aligned</option> <option value="excludeAligned">Exclude aligned</option> <option value="includeReadList">Include read list</option> <option value="excludeReadList">Exclude read list</option> </param> <when value="includeAligned"/> <!-- do nothing --> <when value="excludeAligned"/> <!-- do nothing --> <when value="includeReadList"> <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/> </when> <when value="excludeReadList"> <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> <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"/> <param name="filter" value="includeReadList"/> <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> <param name="validation_stringency" value="LENIENT"/> <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="4"/> </test> <test> <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> <param name="filter" value="excludeReadList"/> <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> <param name="validation_stringency" value="LENIENT"/> <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="4"/> </test> </tests> <help> **Purpose** Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. ------ .. class:: warningmark **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. @dataset_collections@ @description@ FILTER=Filter Filter. Required. Possible values: 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)], excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only. (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 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]} 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. @more_info@ </help> <expand macro="citations" /> </tool>