Mercurial > repos > devteam > picard
view picard_FilterSamReads.xml @ 6:961236c5ec73 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author | devteam |
---|---|
date | Mon, 09 Nov 2015 11:49:09 -0500 |
parents | 52fdfc45590a |
children | 08f69add4d06 |
line wrap: on
line source
<tool name="FilterSamReads" id="picard_FilterSamReads" version="@TOOL_VERSION@.0"> <description>include or exclude aligned and unaligned reads and read lists</description> <macros> <import>picard_macros.xml</import> </macros> <expand macro="requirements" /> <command> @java_options@ ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order java -jar \$JAVA_JAR_PATH/picard.jar SortSam INPUT="${inputFile}" OUTPUT=query_sorted_bam.bam SORT_ORDER=queryname VALIDATION_STRINGENCY=LENIENT QUIET=true VERBOSITY=ERROR && java -jar \$JAVA_JAR_PATH/picard.jar FilterSamReads INPUT=query_sorted_bam.bam FILTER="${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"/> <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="2"/> </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="2"/> </test> </tests> <stdio> <exit_code range="1:" level="fatal"/> </stdio> <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> </tool>