annotate energy-estimation-utility.xml @ 3:cd1bba1c66b3 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 74012d450ef40c04e15171b7ccbd62b03cb2de62

<tool id="energy_estimation_utility" name="energy-estimation-utility" version="1.6.3-1">
    <description>Estimate the maximal energy a segment needs to assign to become part of the optimal structure using segmentation-fold</description>
    
    <requirements>
        <requirement type="package" version="1.6.3">segmentation-fold</requirement>
        <requirement type="package" version="2.7.10">python</requirement>
    </requirements>
    
    <stdio></stdio>
    
    <version_command>segmentation-fold --version | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
    
    <command><![CDATA[
        energy-estimation-utility
            #if $parameters.use_custom_xml == "true"
                -x "${parameters.input_xml}"
            #else
                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
            #end if
            
            -r ${randomization.shuffle_n_times}
        > "${output_list}"
    ]]></command>
    
    <inputs>
        <conditional name="parameters">
            <param name="use_custom_xml"
                type="boolean"
                truevalue="true"
                falsevalue="false"
                selected="false"
                label="Use segment definition from history" />

            <when value="false" />
            <when value="true">
                <param name="input_xml"
                    type="data"
                    format="xml"
                    multiple="false"
                    argument="-x"
                    label="Custom 'segments.xml'-syntaxed file" />
            </when>
        </conditional>
        
        <conditional name="randomization">
            <param name="do_randomization"
                type="boolean"
                truevalue="true"
                falsevalue="false"
                selected="false"
                label="Randomly shuffle the sequence(s) instead"
                help="This can be helpful in determining a baseline of observing an energy parameter by chance" />

            <when value="false">
                <param name="shuffle_n_times"
                       type="hidden"
                       value="0"/>
            </when>
            <when value="true">
                <param name="shuffle_n_times"
                       type="integer"
                       min="0"
                       value="10" 
                       argument="-r"
                       label="Number of times the sequences have to be shuffled and energy parameters have to be estimated on" />
            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data format="text" name="output_list" label="${tool.name}" />
    </outputs>
    
    <tests>
        <test>
            <param  name="use_custom_xml" value="true" />
            <param  name="input_xml" value="segments_truncated.xml" ftype="xml" />
            <param  name="do_randomization" value="false" />
            <param  name="shuffle_n_times" value="0" />
            
            <output name="output_list" file="segments_truncated.out.txt" lines_diff="2" /><!-- Accept rounding errors by diff CPU's etc. -->
        </test>
        <test>
            <param  name="use_custom_xml" value="true" />
            <param  name="input_xml" value="segments_truncated.xml" ftype="xml" />
            <param  name="do_randomization" value="false" />
            <param  name="shuffle_n_times" value="1" />
            
            <output name="output_list" file="segments_truncated.2.out.txt" lines_diff="10" />
        </test>
    </tests>
    
    <help><![CDATA[
The tool uses the sequences from the xml file.
    ]]></help>
    
    <citations>
        <citation type="bibtex">
           @mastersthesis{mastersthesis,
              author       = {Youri Hoogstrate}, 
              title        = {An algorithm for predicting RNA 2D structures including K-turns},
              school       = {University of Technology Delft, Leiden University},
              year         = 2012,
              address      = {},
              month        = 11,
              note         = {Research assignment for Master Computer-science},
              url          = { https://yh-kt-fold.googlecode.com/files/Report.pdf }
            }
        </citation>
    </citations>
</tool>