comparison mut2read.xml @ 84:e46d5e377760 draft

planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty

83:8cec772c0bf1

<?xml version="1.0" encoding="UTF-8"?>
<tool id="mut2read" name="DCS mutations to tags/reads:" version="3.0.0" profile="19.01">
    <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description>
    <macros>
        <import>va_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
        python '$__tool_directory__/mut2read.py' 
        --mutFile '$file1'
        --bamFile bam_input.bam
        --familiesFile '$file3'
        --outputFastq '$output_fastq' 
        --outputJson '$output_json'
    ]]>
    </command>
    <inputs>
        <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See the Help section below for a detailed explanation."/>
        <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
        <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
    </inputs>
    <outputs>
        <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
        <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
    </outputs>

**What it does**

Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a 
tabular file with aligned families as input and prints all tags of reads that 
carry a mutation or have the reference allele to a user-specified output file and creates a fastq file of 
reads of tags with a mutation and the reference allele.

**Input** 

**Dataset 1:** VCF file with duplex consensus sequence (DCS) mutations. E.g. 
generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.

84:e46d5e377760

<?xml version="1.0" encoding="UTF-8"?>
<tool id="mut2read" name="DCS mutations to tags/reads:" version="3.1.0" profile="19.01">
    <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description>
    <macros>
        <import>va_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
        python '$__tool_directory__/mut2read.py' 
        --mutFile '$file1'
        --bamFile bam_input.bam
        --familiesFile '$file3'
        $refalttiers
        --outputFastq '$output_fastq' 
        --outputJson '$output_json'
    ]]>
    </command>
    <inputs>
        <param name="file1" type="data" format="vcf" label="DCS Mutation File" optional="false" help="VCF file with DCS mutations. See the Help section below for a detailed explanation."/>
        <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/>
        <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/>
        <param name="refalttiers" type="boolean" label="Extract tiers also for reference allele" truevalue="--refalttiers" falsevalue="" checked="False" help="Extracts tier information for the alternate and reference allele. Note that this will increase the running time of the tool. Otherwise only the tier information for the alternate allele is extracted."/>
    </inputs>
    <outputs>
        <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/>
        <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/>
    </outputs>

**What it does**

Takes a VCF file with mutations, a BAM file of aligned DCS reads, and a 
tabular file with aligned families as input and prints all tags of reads that 
carry a mutation or have the reference allele to a user-specified output file and creates a fastq file of 
reads of tags with a mutation (and optional the reference allele).

**Input** 

**Dataset 1:** VCF file with duplex consensus sequence (DCS) mutations. E.g. 
generated by the `FreeBayes <https://arxiv.org/abs/1207.3907>`_ or `LoFreq <https://academic.oup.com/nar/article/40/22/11189/1152727>`_ variant caller.