comparison tomo/tomo_reduce.xml @ 1:84a215623d9e draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit f4980be19456f3f51758e06e2eb7520924ce1e3a

1:84a215623d9e

<tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
    <description>Reduce tomography images</description>
    <macros>
        <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
            '$__tool_directory__/pipeline_reduce_nexus.yaml'
        #end if
        ]]>
    </command>
    <configfiles>
        <configfile name="tool_config">
            <![CDATA[#slurp
                #if str($map.type_selector) == "YAML"
                    #if str($detector.type_selector) == "andor2"
                        #cat andor2.yaml
                    #elif str($detector.type_selector) == "manta"
                        #cat manta.yaml
                    #else str($detector.type_selector) == "retiga"
                        #cat retiga.yaml
                    #end if
                #end if
                #echo 'img_x_bounds:' #
                #if str($img_x_bounds.type_selector) == "full_range"
                    #echo '- -1'
                    #echo '- -1'
                #else
                    #echo '- ' + str($img_x_bounds.low)
                    #echo '- ' + str($img_x_bounds.upp)
                #end if
            ]]>
        </configfile>
    </configfiles>
    <inputs>
        <conditional name="map">
            <param name="type_selector" type="select" display="radio" label="Choose map file type">
                <option value="yaml">YAML</option>
                <option value="nexus">NeXus</option>
            </param>
            <when value="yaml">
                <param name="input_file" type="data" format="yaml" optional="false" label="Map config file"/>
                <conditional name="detector">
                    <param name="type_selector" type="select" display="radio" label="Choose detector prefix">
                        <option value="andor2">andor2</option>
                        <option value="manta">manta</option>
                        <option value="retiga">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>
        </conditional>
        <conditional name="img_x_bounds">
            <param name="type_selector" type="select" label="Choose vertical detector image bounds">
                <option value="full_range" selected="true">Use the full image range</option>
                <option value="enter_range">Manually enter the image range</option>
            </param>
            <when value="full_range"/>
            <when value="enter_range">
                <param name="low" type="integer" value="-1" optional="false" label="Lower image range index"/>
                <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]

options:
  -h, --help       show this help message and exit
  --config CONFIG  Input configuration file
  --verbose        verbose output

        ]]>
    </help>
    <expand macro="citations"/>
</tool>