view tomo/tomo_reduce.xml @ 139:59d672fde7fd draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 3d091903055c4f157d9e266f8af0157fac1c95fd-dirty

<tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
    <description>Reduce tomography images</description>
    <macros>
        <import>../macros.xml</import>
        <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"
            cp $input_file map.yaml &&
            #if str($map.detector.type_selector) == "from_file"
                cat $map.detector.detector_file $tool_config > reduce.yaml &&
            #elif str($map.detector.type_selector) == "manual"
                cat $tool_config > reduce.yaml &&
            #else
                cat $__tool_directory__/$map.detector.type_selector $tool_config > reduce.yaml &&
            #end if
        #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
            $__tool_directory__/pipeline_reduce_nexus.yaml
        #end if
        ]]>
    </command>
    <configfiles>
        <configfile name="tool_config">
            <![CDATA[#slurp
#if str($map.detector.type_selector) == "manual"
#echo 'detector:' #
#echo '  prefix: ' + str($map.detector.prefix) #
#echo '  rows: ' + str($map.detector.rows) #
#echo '  columns: ' + str($map.detector.columns) #
#echo '  pixel_size:' #
#echo '  - ' + str($map.detector.x_pixelsize) #
#echo '  - ' + str($map.detector.y_pixelsize) #
#echo '  lens_magnification: ' + str($map.detector.lens_magnification) #
#end if
#echo 'img_x_bounds:' #
#if str($img_x_bounds.type_selector) == "enter_range"
#echo '- ' + str($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">
                        <option value="andor2.yaml">andor2</option>
                        <option value="manta.yaml">manta</option>
                        <option value="retiga.yaml">retiga</option>
                        <option value="manual">enter manually</option>
                        <option value="from_file">from file</option>
                    </param>
                    <when value="andor2.yaml"/>
                    <when value="manta.yaml"/>
                    <when value="retiga.yaml"/>
                    <when value="manual">
                        <param name="prefix" type="text" label="Detector prefix in SPEC file"/>
                        <param name="rows" type="integer" value="" optional="false" min="1" label="Number of pixel rows on detector"/>
                        <param name="columns" type="integer" value="" optional="false" min="1" label="Number of pixel columns on detector"/>
                        <param name="x_pixelsize" type="float" value="" optional="false" min="0.0" label="Row pixel size of detector in mm"/>
                        <param name="y_pixelsize" type="float" value="" optional="false" min="0.0" label="Column pixel size of detector in mm"/>
                        <param name="lens_magnification" type="float" value="1.0" optional="true" label="Detector lens magnification"/>
                    </when>
                    <when value="from_file">
                        <param name="detector_file" type="data" format="yaml" optional="false" label="Detector config file"/>
                    </when>
                </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="" optional="false" min="0" label="Lower image range index"/>
                <param name="upp" type="integer" value="" optional="false" min="0" 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>