comparison manta_macros.xml @ 3:d648e40c6da9 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"

2:6a69e5d7c21f

<macros>

    <token name="@VERSION@">1.6</token>
    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy4</token>
    <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>

    <token name="@set_reference_fasta_filename@"><![CDATA[
    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
    ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
    samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 &&
    #else:
    #set $reference_fasta_filename = str( $reference_source.index.fields.path )
    #end if
    ]]></token>

    #if str( $configuration.configuration_switch ) == "Custom_config_file":
    #set $config_file = '$configuration.CustomConfigFile'
    #else if str( $configuration.configuration_switch )== "Customized":
    #set $config_file = '$configuration.Customized'
    #else:
    #set $config_file = $__tool_directory__ + '/configManta.py.ini'
    #end if
    ]]></token>


    <xml name="requirements">

3:d648e40c6da9

<macros>

    <token name="@VERSION@">1.6</token>
    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy5</token>
    <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>

    <token name="@set_reference_fasta_filename@"><![CDATA[
    #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 Manta" >&2 &&
    #else:
    #set $reference_fasta_filename = str( $reference_source.index.fields.path )
    #end if
    ]]></token>

    #if str( $configuration.configuration_switch ) == "Custom_config_file":
    #set $config_file = '$configuration.CustomConfigFile'
    #else if str( $configuration.configuration_switch )== "Customized":
    #set $config_file = '$configuration.Customized'
    #else:
    #set $config_file = 'configManta.py.ini'
    #end if
    ]]></token>


    <xml name="requirements">