view tomo/tomo_reconstruct.xml @ 124:020caca70a9a draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 6697892ecc504b00077394d0c167431ec3ac12f7-dirty

<tool id="CHAP_tomo_reconstruct" name="Tomo Reconstruct" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
    <description>Reconstruct tomography stacks</description>
    <macros>
        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        mkdir tomo_reconstruct_plots;
        cp $input_file reduced.nex &&
        cp $center_file centers.yaml &&
        cp $tool_config reconstruct.yaml &&
        CHAP --config 
        $__tool_directory__/pipeline_reconstruct.yaml
        ]]>
    </command>
    <configfiles>
        <configfile name="tool_config">
            <![CDATA[#slurp
#if str($x_bounds.type_selector) == "enter_range"
#echo 'x_bounds:' #
#echo '- ' + str($x_bounds.low) #
#echo '- ' + str($x_bounds.upp) #
#end if
#if str($y_bounds.type_selector) == "enter_range"
#echo 'y_bounds:' #
#echo '- ' + str($y_bounds.low) #
#echo '- ' + str($y_bounds.upp) #
#end if
#echo 'secondary_iters: ' + str($secondary_iters) #
#echo 'remove_stripe_sigma: ' + str($remove_stripe_sigma) #
#echo 'ring_width: ' + str($ring_width) #
            ]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="input_file" type="data" format="nex" optional="false" label="Reduce tomography data file"/>
        <param name="center_file" type="data" format="yaml" optional="false" label="Rotation axis centers data file"/>
        <conditional name="x_bounds">
            <param name="type_selector" type="select" label="Choose reconstructed image range in the x-direction">
                <option value="full_range" selected="true">Use the full image range</option>
                <option value="enter_range">Manually enter the image range in the x-direction</option>
            </param>
            <when value="full_range"/>
            <when value="enter_range">
                <param name="low" type="integer" value="" optional="false" min="0" label="Lower image x-range index"/>
                <param name="upp" type="integer" value="" optional="false" min="0" label="Upper image x-range index"/>
            </when>
        </conditional>
        <conditional name="y_bounds">
            <param name="type_selector" type="select" label="Choose reconstructed image range in the y-direction">
                <option value="full_range" selected="true">Use the full image range</option>
                <option value="enter_range">Manually enter the image range in the y-direction</option>
            </param>
            <when value="full_range"/>
            <when value="enter_range">
                <param name="low" type="integer" value="" optional="false" min="0" label="Lower image y-range index"/>
                <param name="upp" type="integer" value="" optional="false" min="0" label="Upper image y-range index"/>
            </when>
        </conditional>
        <param name="secondary_iters" type="integer" value="0" optional="false" min="0" label="Number of secondary iterations"/>
        <param name="remove_stripe_sigma" type="float" value="0.05" optional="false" min="0" label="Damping parameter in horizontal stripe removal"/>
        <param name="ring_width" type="float" value="1" optional="false" min="1" label="Maximum filtered ring width in pixels"/>
    </inputs>
    <outputs>
        <data name="tool_config" format="yaml" label="Tool config" from_work_dir="reconstruct.yaml" hidden="false"/>
        <collection name="tomo_reconstruct_plots" type="list" label="Data reconstruction images">
            <discover_datasets pattern="__name_and_ext__" directory="tomo_reconstruct_plots"/>
        </collection>
        <data name="output_file" format="nex" label="Reconstructed 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>