view scan-for-segments.xml @ 4:21e619c46cb5 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 61ba605ef9eb63914a248fe389860daa2249af69

<tool id="scan_for_segments" name="scan-for-segments" version="1.6.0">
    <description>Scan for the presence of segments in sequences using segmentation-fold</description>
    
    <requirements>
        <requirement type="package" version="1.1.0">segmentation-fold</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[
        scan-for-segments
            -T \${GALAXY_SLOTS:-4}
            #if $parameters.use_custom_xml == "true"
                -x "${parameters.input_xml}"
            #else
                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
            #end if
            -p "in-depth"
            "${input_fasta}"
            
            >   $output_list
    ]]></command>

    <inputs>
        <param name="input_fasta"
               type="data"
               format="fasta"
               argument="-f"
               label="Fasta file with RNA-sequece" />

        <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>
    </inputs>

    <outputs>
        <data format="text" name="output_list" label="${tool.name} on ${str($input_fasta.hid) + ': ' + $input_fasta.name}" />
    </outputs>

    <tests>
        <test>
            <param name="input_fasta" value="SNORD13-revised.fa" ftype="fasta" />
            <param name="use_custom_xml" value="false" ftype="fasta" />
            
            <output name="output_list" file="SNORD13-revised.scan-for-segments.txt" />
        </test>
        <test>
            <param name="input_fasta" value="SNORD48-revised.fa" ftype="fasta" />
            <param name="use_custom_xml" value="false" ftype="fasta" />
            
            <output name="output_list" file="SNORD48-revised.scan-for-segments.txt" />
        </test>
        <test>
            <param name="input_fasta" value="SNORD114-4-revised.fa" ftype="fasta" />
            <param name="use_custom_xml" value="false" ftype="fasta" />
            
            <output name="output_list" file="SNORD114-4-revised.scan-for-segments.txt" />
        </test>
        <test>
            <param name="input_fasta" value="SNORD118-revised.fa" ftype="fasta" />
            <param name="use_custom_xml" value="false" ftype="fasta" />
            
            <output name="output_list" file="SNORD118-revised.scan-for-segments.txt" />
        </test>
    </tests>
    
    <help><![CDATA[
This is an utility of the segmentation-fold package that allows to scan for the presence of certain segments.
If present, it will also scan for the Gibbs free energy necessairy the segment has to provide to contribute to the optimal structure.
    ]]></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>