Mercurial > repos > yusuf > filter_bam_list
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author | Yusuf Ali <ali@yusuf.email> |
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date | Wed, 25 Mar 2015 13:33:46 -0600 |
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<?xml version="1.0"?> <tool id="filter_bam_by_list_1" name="Filter a BAM file"> <description>against a list of desired genomic regions, by name</description> <version_string>echo 1.0.0</version_string> <command interpreter="perl">filter_bam_by_list $bam_file $named_gene_regions_bed ## Handle reference file. #if $geneNameSource.source == "file": $geneNameSource.file_of_names #else: "${geneNameSource.name_list}" #end if $filtered_bam_file $retained_regions_bed $samtools_messages</command> <inputs> <param format="bam" name="bam_file" type="data" label="Source BAM (mapped reads) file"/> <param format="bed" name="named_gene_regions_bed" type="data" label="BED file with names for genomic regions (e.g. the UCSC hg19 refFlat gene names file available under 'Shared Data Libraries' -> 'Genomic coding sequence regions')"/> <conditional name="geneNameSource"> <param name="source" type="select" label="How would you like to specify the list of target region names?"> <option value="file">A file</option> <option value="list">A list</option> </param> <when value="file"> <param format="text" name="file_of_names" type="data" label="Text file with target region names (usually gene names), one per line" help="Mapped reads in regions with any of these names are retained"/> </when> <when value="list"> <param name="name_list" type="text" label="Space separated list of target region names (usually gene names)" help="Mapped reads in regions with any of these names are retained"/> </when> </conditional> </inputs> <outputs> <data name="filtered_bam_file" format="bam" type="data" label="Reads mapped to target regions"/> <data name="retained_regions_bed" format="bed" type="data" label="BED file of retained regions"/> <data name="samtools_messages" format="text" type="data" label="Samtools messages"/> </outputs> <tests/> <help> This tool retains sequence reads of a BAM file that map to genomics regions matching any of the labels in the "names" file. This is useful for example to report only a subset of an exome run that corresponds to a set of genes of interest. The names file should have one name per line. </help> </tool>