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1 <?xml version="1.0"?>
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2
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3 <tool id="call_miseq_vars" name="Call miSeq variants">
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4 <description>using a BAM file</description>
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5 <version_string>echo 1.0.0</version_string>
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6 <command interpreter="perl">call_miseq_variants $__tool_data_path__ geno . $inputBAM ${targetBED}.bed ${ref_genome}.bed ${ref_genome}.fa 12</command>
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7 <inputs>
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8 <param format="bam" name="inputBAM" type="data" label="Source BAM (mapped and realigned reads) file"/>
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9 <param name="ref_genome" type="genomebuild" label="Reference genome" help="against which the reads were aligned"/>
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10 <param name="targetBED" type="select" display="radio" dynamic_options="kit_fileOptions()" label="The enrichment (capture) kit used for the sequencing experiment"/>
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11 </inputs>
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12 <outputs>
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13 <data format="achri_snp_table" label="Confident genotypes" name="confident_genotypes" from_work_dir="geno.combined.collapsed.confident.hgvs.txt"/>
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14 <data format="achri_snp_table" label="Marginal genotypes" name="marginal_genotypes" from_work_dir="geno.combined.collapsed.marginal.hgvs.txt"/>
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15 <data format="text" label="Genotyping log" name="genotyping log" from_work_dir="geno.call_variants.log.txt"/>
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16 </outputs>
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17
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18 <!-- the following code populates the selection from the public dbSNP datasets available in the local Galaxy installation -->
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19 <code file="capture_kits.py"/>
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20 <tests/>
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21
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22 <help>
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23 This tool runs a BAM file against multiple genotypers (FreeBayes 0.8.7, GATKHaplotypeCaller 3.1) and generates a consensus (confident) table of variant calls,
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24 including caveats about haplotype phase inconsistencies and other potential false positive indicators.
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25 </help>
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26
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27 </tool>
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