annotate FilterBAMByNamesList.xml @ 0:42af0b971c55 default tip

intial commit

<?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' -&gt; '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>