Mercurial > repos > yusuf > filter_bam_list
comparison FilterBAMByNamesList.xml @ 0:42af0b971c55 default tip
intial commit
| author | Yusuf Ali <ali@yusuf.email> |
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| date | Wed, 25 Mar 2015 13:33:46 -0600 |
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| -1:000000000000 | 0:42af0b971c55 |
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| 1 <?xml version="1.0"?> | |
| 2 | |
| 3 <tool id="filter_bam_by_list_1" name="Filter a BAM file"> | |
| 4 <description>against a list of desired genomic regions, by name</description> | |
| 5 <version_string>echo 1.0.0</version_string> | |
| 6 <command interpreter="perl">filter_bam_by_list $bam_file $named_gene_regions_bed | |
| 7 ## Handle reference file. | |
| 8 #if $geneNameSource.source == "file": | |
| 9 $geneNameSource.file_of_names | |
| 10 #else: | |
| 11 "${geneNameSource.name_list}" | |
| 12 #end if | |
| 13 $filtered_bam_file $retained_regions_bed $samtools_messages</command> | |
| 14 <inputs> | |
| 15 <param format="bam" name="bam_file" type="data" label="Source BAM (mapped reads) file"/> | |
| 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')"/> | |
| 17 <conditional name="geneNameSource"> | |
| 18 <param name="source" type="select" label="How would you like to specify the list of target region names?"> | |
| 19 <option value="file">A file</option> | |
| 20 <option value="list">A list</option> | |
| 21 </param> | |
| 22 <when value="file"> | |
| 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"/> | |
| 24 </when> | |
| 25 <when value="list"> | |
| 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"/> | |
| 27 </when> | |
| 28 </conditional> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data name="filtered_bam_file" format="bam" type="data" label="Reads mapped to target regions"/> | |
| 32 <data name="retained_regions_bed" format="bed" type="data" label="BED file of retained regions"/> | |
| 33 <data name="samtools_messages" format="text" type="data" label="Samtools messages"/> | |
| 34 </outputs> | |
| 35 | |
| 36 <tests/> | |
| 37 | |
| 38 <help> | |
| 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 | |
| 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. | |
| 41 </help> | |
| 42 | |
| 43 </tool> |