comparison leftalign.xml @ 28:977a5301b66d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214

27:9f164587a92f

<?xml version="1.0"?>
<tool id="bamleftalign" name="BamLeftAlign" version="@DEPENDENCY_VERSION@-1">
    <description> indels in BAM datasets</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.0.2.29">freebayes</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        ##set up input files
        #set $reference_fasta_filename = "localref.fa"
        #if str( $reference_source.reference_source_selector ) == "history":
            ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
            samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for leftalign" >&2 &&

28:977a5301b66d

<?xml version="1.0"?>
<tool id="bamleftalign" name="BamLeftAlign" version="@DEPENDENCY_VERSION@-2">
    <description> indels in BAM datasets</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        ##set up input files
        #set $reference_fasta_filename = "localref.fa"
        #if str( $reference_source.reference_source_selector ) == "history":
            ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
            samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for leftalign" >&2 &&