comparison tomo/tomo_reduce.xml @ 40:eef6fd513736 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit eda217fb0afe5af50380a24b578c668db9c004f4-dirty

39:d0d62ad6daa4

        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        mkdir tomo_reduce_plots;
        pip --exists-action i install --target='/nfs/chess/galaxy-dev/var/dependencies/_conda/envs' certif-pyspec==1.5.3
        #if str($map.type_selector) == "yaml"
            cp $input_file map.yaml &&
            cat $__tool_directory__/andor2.yaml $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">

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/>
        <collection name="tomo_reduce_plots" type="list" label="Data reduction images">
            <discover_datasets pattern="__name_and_ext__" directory="tomo_reduce_plots"/>
        </collection>
        <data name="output_file" format="nex" label="Reduced tomography data" from_work_dir="output.nex"/>
    </outputs>
    <help>
        <![CDATA[
        usage: PROG [-h] [--config CONFIG] [--verbose]

40:eef6fd513736

        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        pip --exists-action i install --target='/nfs/chess/galaxy-dev/var/dependencies/_conda/envs' certif-pyspec==1.5.3
        #if str($map.type_selector) == "yaml"
            cp $input_file map.yaml &&
            cat $__tool_directory__/andor2.yaml $tool_config > reduce.yaml
        #else
            cp $input_file setup.nex &&
            cp $tool_config reduce.yaml
        #end if
        ]]>
    </command>
    <configfiles>
        <configfile name="tool_config">

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reduce.yaml" hidden="false"/>
    </outputs>
    <help>
        <![CDATA[
        usage: PROG [-h] [--config CONFIG] [--verbose]