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1 <?xml version="1.0"?>
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2
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3 <tool id="dedup_realign_bam_1" name="Deduplicate and realign a BAM file(s)">
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4 <description>using samtools and GATK</description>
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5 <version_string>echo 1.0.0</version_string>
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6 <command interpreter="perl">prep_bams $__tool_data_path__ $messages $ref_genome\.fa ${__new_file_path__} $prepped_bam_file $input_bam_file
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7 #for $i in $inputs
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8 ${i.input}
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9 #end for
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10 </command>
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11 <inputs>
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12 <param name="ref_genome" type="genomebuild" label="Reference genome" help="against which the reads were mapped"/>
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13 <param format="bam" name="input_bam_file" type="data" label="Source BAM (mapped reads) file" help="Need to merge multiple input BAM files for one sample? Use controls below."/>
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14 <repeat name="inputs" title="Input BAM Files">
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15 <param name="input" label="Additional BAM file to merge" type="data" format="bam" />
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16 </repeat>
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17
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18 </inputs>
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19 <outputs>
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20 <data name="prepped_bam_file" format="bam" type="data" label="Deduped and realigned mapped reads"/>
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21 <data name="messages" format="text" type="data" label="Prep process log messages"/>
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22 </outputs>
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23
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24 <tests/>
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25
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26 <help>
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27 This tool runs a set of processes to first optionally merge BAMs, then deduplicate (samtools) and realign (GATK) the reads mapped to a reference genome.
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28 This is important for genotyping studies. While these steps could be run independently in a workflow,
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29 an enormous amount of intermediate data files are generated. This tool cleans up those intermediate files.
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30 </help>
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31
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32 </tool>
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