comparison mut2sscs.xml @ 1:3556001ff2db draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 60dc8db809909edf44d662683b1f392b9d5964bf"

0:8d29173d49a9

<?xml version="1.0" encoding="UTF-8"?>
<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="1.0.0" profile="19.01">
    <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</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>
    </requirements>
    <command><![CDATA[
        ln -s '$file2' bam_input.bam &&
        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
        python '$__tool_directory__/mut2sscs.py' 
        --mutFile '$file1'

1:3556001ff2db

<?xml version="1.0" encoding="UTF-8"?>
<tool id="mut2sscs" name="DCS mutations to SSCS stats:" version="1.0.1" profile="19.01">
    <description>Extracts all tags from the single stranded consensus sequence (SSCS) bam file that carry a mutation at the same position a mutation is called in the duplex consensus sequence (DCS) and calculates their frequencies</description>
    <macros>
        <import>va_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
        ln -s '$file2' bam_input.bam &&
        ln -s '${file2.metadata.bam_index}' bam_input.bam.bai &&
        python '$__tool_directory__/mut2sscs.py' 
        --mutFile '$file1'