comparison tomo/tomo_reduce.xml @ 79:7638a2c68b7f draft

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

78:d0bc5f9dc4c9

        <![CDATA[
        mkdir tomo_reduce_plots;
        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
        #if str($map.type_selector) == "yaml"
            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">

                    <param name="type_selector" type="select" display="radio" label="Choose detector prefix">
                        <option value="andor2.yaml">andor2</option>
                        <option value="manta.yaml">manta</option>
                        <option value="retiga.yaml">retiga</option>
                    </param>
                    <when value="andor2"/>
                    <when value="manta"/>
                    <when value="retiga"/>
                </conditional>
            </when>
            <when value="nexus">
                <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/>
            </when>

79:7638a2c68b7f

        <![CDATA[
        mkdir tomo_reduce_plots;
        $__tool_directory__/../pip_install.sh 'certif-pyspec==1.5.3' &&
        #if str($map.type_selector) == "yaml"
            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
        ]]>
    </command>
    <configfiles>
        <configfile name="tool_config">

                    <param name="type_selector" type="select" display="radio" label="Choose detector prefix">
                        <option value="andor2.yaml">andor2</option>
                        <option value="manta.yaml">manta</option>
                        <option value="retiga.yaml">retiga</option>
                    </param>
                    <when value="andor2.yaml"/>
                    <when value="manta.yaml"/>
                    <when value="retiga.yaml"/>
                </conditional>
            </when>
            <when value="nexus">
                <param name="input_file" type="data" format="nex" optional="false" label="Tomography setup file"/>
            </when>