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1 <?xml version="1.0"?>
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2
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3 <tool id="filter_bam_by_list_1" name="Filter a BAM file">
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4 <description>against a list of desired genomic regions, by name</description>
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5 <version_string>echo 1.0.0</version_string>
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6 <command interpreter="perl">filter_bam_by_list $bam_file $named_gene_regions_bed
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7 ## Handle reference file.
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8 #if $geneNameSource.source == "file":
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9 $geneNameSource.file_of_names
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10 #else:
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11 "${geneNameSource.name_list}"
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12 #end if
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13 $filtered_bam_file $retained_regions_bed $samtools_messages</command>
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14 <inputs>
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15 <param format="bam" name="bam_file" type="data" label="Source BAM (mapped reads) file"/>
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16 <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')"/>
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17 <conditional name="geneNameSource">
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18 <param name="source" type="select" label="How would you like to specify the list of target region names?">
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19 <option value="file">A file</option>
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20 <option value="list">A list</option>
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21 </param>
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22 <when value="file">
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23 <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"/>
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24 </when>
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25 <when value="list">
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26 <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"/>
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27 </when>
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28 </conditional>
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29 </inputs>
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30 <outputs>
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31 <data name="filtered_bam_file" format="bam" type="data" label="Reads mapped to target regions"/>
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32 <data name="retained_regions_bed" format="bed" type="data" label="BED file of retained regions"/>
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33 <data name="samtools_messages" format="text" type="data" label="Samtools messages"/>
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34 </outputs>
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35
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36 <tests/>
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37
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38 <help>
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39 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
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40 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.
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41 </help>
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42
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43 </tool>
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