comparison freebayes.xml @ 34:a7c9782130e8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit be1c2e9e056710ef8b1110a121dc38c6e06dbbee"

33:04fa42777df9

<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1">
    <description>bayesian genetic variant detector</description>
    <xrefs>
        <xref type="bio.tools">freebayes</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="5.1.0">gawk</requirement>
        <requirement type="package" version="20211022">parallel</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
            <param name="options_type_selector" value="simple"/>
            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

34:a7c9782130e8

<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
    <description>bayesian genetic variant detector</description>
    <xrefs>
        <xref type="bio.tools">freebayes</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="5.1.0">gawk</requirement>
        <requirement type="package" version="20211222">parallel</requirement>
    </expand>
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
            <param name="options_type_selector" value="simple"/>
            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**