comparison tomo/tomo_reduce.xml @ 83:9b6e931e0de0 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 64d735e72badb6466fcf32843328300887a4a46e-dirty

82:6b20bd5d489a

        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3'
        ]]>
    </command>
    <configfiles>
        <configfile name="tool_config">
            <![CDATA[#slurp

83:9b6e931e0de0

        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        mkdir tomo_reduce_plots;
        #if str($map.type_selector) == "yaml"
            $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
            cp $input_file map.yaml &&
            cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml &&
        #else
            cp $input_file setup.nex &&
            cp $tool_config reduce.yaml &&
        #end if
        CHAP --config
        #if str($map.type_selector) == "yaml"
            $__tool_directory__/pipeline_reduce_yaml.yaml
        #else
            $__tool_directory__/pipeline_reduce_nexus.yaml
        #end if
        ]]>
    </command>
    <configfiles>
        <configfile name="tool_config">
            <![CDATA[#slurp