comparison tomo/tomo_reduce.xml @ 5:47a0648cdfd1 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 3e8c1c54d5e12fdbc4f6c5cdae88b6d054db7c45

4:ed26d2bb9723

        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        mkdir tomo_reduce_plots;
        pip --exists-action i install certif-pyspec==1.5.3 &&
        #if str($map.type_selector) == "YAML"
            cp '$input_file' map.yaml &&
        #else
            cp '$input_file' setup.nex &&
        #end if
        cp '$tool_config' reduce.yaml &&
        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

                <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index"/>
            </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]

5:47a0648cdfd1

        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
            cp '$input_file' output.yaml
        ]]>
    </command>
    <configfiles>
        <configfile name="tool_config">
            <![CDATA[#slurp

                <param name="upp" type="integer" value="-1" optional="false" label="Upper image range index"/>
            </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"/>
        -->
        <data name="output_file" format="yaml" label="Test output" from_work_dir="output.yaml"/>
    </outputs>
    <help>
        <![CDATA[
        usage: PROG [-h] [--config CONFIG] [--verbose]