comparison read2mut.xml @ 72:3691922baa08 draft

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

71:8664c0aa91c3

<?xml version="1.0" encoding="UTF-8"?>
<tool id="read2mut" name="Call specific mutations in reads:" version="2.1.2" profile="17.01">
    <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
    <macros>
        <import>va_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.7">python</requirement>
        <requirement type="package" version="1.4.0">matplotlib</requirement>
        <requirement type="package" version="0.15">pysam</requirement>
        <requirement type="package" version="1.1.0">xlsxwriter</requirement>
        <requirement type="package" version="0.11.6">cyvcf2</requirement>
    </requirements>
    <command><![CDATA[
        ln -s '$file2' bam_input.bam &&
        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
        python '$__tool_directory__/read2mut.py' 

72:3691922baa08

<?xml version="1.0" encoding="UTF-8"?>
<tool id="read2mut" name="Call specific mutations in reads:" version="2.1.2" profile="19.01">
    <description>Looks for reads with mutation at known positions and calculates frequencies and stats.</description>
    <macros>
        <import>va_macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.1.0">xlsxwriter</requirement>
    </expand>
    </requirements>
    <command><![CDATA[
        ln -s '$file2' bam_input.bam &&
        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
        python '$__tool_directory__/read2mut.py'