view tomo/tomo_find_center.xml @ 134:96f74c637a36 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty

<tool id="CHAP_tomo_find_center" name="Tomo Find Center" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
    <description>Find rotation axis centers for the tomography stacks</description>
    <macros>
        <import>tomo_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        mkdir tomo_find_center_plots;
        cp $input_file reduced.nex &&
        cp $tool_config find_center.yaml &&
        CHAP --config 
        $__tool_directory__/pipeline_find_center.yaml
        ]]>
    </command>
    <configfiles>
        <configfile name="tool_config">
            <![CDATA[#slurp
#if str($center_rows.type_selector) == "enter_range"
#echo 'lower_row: ' + str($center_rows.low) #
#echo 'upper_row: ' + str($center_rows.upp) #
#end if
#echo 'gaussian_sigma: ' + str($gaussian_sigma) #
#echo 'ring_width: ' + str($ring_width) #
            ]]>
        </configfile>
    </configfiles>
    <inputs>
        <param name="input_file" type="data" format="nex" optional="false" label="Reduce tomography data file"/>
        <conditional name="center_rows">
            <param name="type_selector" type="select" label="Choose axis center image rows">
                <option value="full_range" selected="true">Use the first and last detector row</option>
                <option value="enter_range">Manually enter the center image rows</option>
            </param>
            <when value="full_range"/>
            <when value="enter_range">
                <param name="low" type="integer" value="" optional="false" min="0" label="Lower detector row index"/>
                <param name="upp" type="integer" value="" optional="false" min="0" label="Upper detector row index"/>
            </when>
        </conditional>
        <param name="gaussian_sigma" type="float" value="0.05" optional="false" min="0" label="Standard deviation for the Gaussian filter"/>
        <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="find_center.yaml" hidden="false"/>
        <collection name="tomo_find_center_plots" type="list" label="Find rotation axis center images">
            <discover_datasets pattern="__name_and_ext__" directory="tomo_find_center_plots"/>
        </collection>
        <data name="output_file" format="yaml" label="Rotation axis centers data" from_work_dir="output.yaml"/>
    </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>