Mercurial > repos > devteam > picard
diff picard_FilterSamReads.xml @ 3:52fdfc45590a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author | devteam |
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date | Thu, 16 Jul 2015 15:32:31 -0400 |
parents | |
children | 08f69add4d06 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_FilterSamReads.xml Thu Jul 16 15:32:31 2015 -0400 @@ -0,0 +1,130 @@ +<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> + +