view scan-for-segments.xml @ 5:fd7f0bf0f5b6 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 3d4c8888c2257e2c01255ea4141fe96bcf6960df

<tool id="scan_for_segments" name="scan-for-segments" version="1.6.2-0">
    <description>Scan for the presence of segments in sequences using segmentation-fold</description>
    
    <requirements>
        <requirement type="package" version="1.6.2">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>