comparison segmentation-fold.xml @ 1:27f670a42ba2 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 4f43c60fd8d3827382fa55c7b6174fa925d7f8e7

0:09e921a25c68

<tool id="segmentation_fold" name="segmentation-fold" version="0.2.0">
    <description>RNA-Folding including predefined segments including K-turns</description>
    
    <requirements>
        <requirement type="package" version="1.0.0">segmentation-fold</requirement>
    </requirements>
    
    <stdio></stdio>
    
    <version_command>segmentation-fold -V | head -n 2 | tail -n 1 | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//'</version_command>
    
    <command><![CDATA[
        segmentation-fold
            
            #if $input.method == "fasta"

            
            -p $predict_segments
            -h $min_hairpin_size
            
            #if $parameters.settings == "default"
                -x "${SEGMENTATION_FOLD_DEFAULT_XML}"
            #else
                -x $parameters.input_xml
            #end if
            
            -t \${GALAXY_SLOTS:-2}
            > $output_dbn
    ]]></command>
    
    <inputs>
        
        <conditional name="input">
            <param name="method" type="select" label="Energy parameters">
                <option value="fasta" selected="true">As FASTA-file</option>
                <option value="text">As text</option>
            </param>

            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data format="dot-bracket" name="output_dbn" label="${tool.name} on ${input.input_fasta.hid + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />
    </outputs>
    
    <tests>
        <test>
            <param  name="input_fasta" value="test_01.fa" ftype="fasta" />

    
    <help><![CDATA[
Segmentation-fold is a bioinformatics application that predicts RNA
2D-structure with an extended version of the Zuker algorithm. This
modification contains a new "structure element" named a segment and is
capable of folding a pre-defined substructure with multiple canonical
or non-canonical pairings.

This allows folding of more complex structures like the K-turns, which
are also part of the implemented free energy tables. These thermodynamic
parameters (free Gibbs energy levels) have been estimated using a
computational approach and therefore lack accuracy.
    ]]></help>
    
    <citations>
        <citation type="bibtex">
           @mastersthesis{mastersthesis,

1:27f670a42ba2

<tool id="segmentation_fold" name="segmentation-fold" version="1.1.0_1">
    <description>RNA-Folding including predefined segments including K-turns</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[
        segmentation-fold
            
            #if $input.method == "fasta"

            
            -p $predict_segments
            -h $min_hairpin_size
            
            #if $parameters.settings == "default"
                -x "\$SEGMENTATION_FOLD_DEFAULT_XML"
            #else
                -x "${parameters.input_xml}"
            #end if
            
            -t \${GALAXY_SLOTS:-4}
            > $output_dbn
    ]]></command>
    
    <inputs>
        <conditional name="input">
            <param name="method" type="select" label="Energy parameters">
                <option value="fasta" selected="true">As FASTA-file</option>
                <option value="text">As text</option>
            </param>

            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data format="dot-bracket" name="output_dbn" label="asdasdasd" />
        <!--<data format="dot-bracket" name="output_dbn" label="${tool.name} on ${str(input.input_fasta.hid) + ': ' + input.input_fasta.name if $input.method == 'fasta' else $input.input_sequence.upper() }" />-->
    </outputs>
    
    <tests>
        <test>
            <param  name="input_fasta" value="test_01.fa" ftype="fasta" />

    
    <help><![CDATA[
Segmentation-fold is a bioinformatics application that predicts RNA
2D-structure with an extended version of the Zuker algorithm. This
modification contains a new "structure element" named a segment and is
capable of folding a pre-defined substructures with multiple canonical
or non-canonical pairings.

This allows folding of more complex structures like K-turns, which are
also part of the implemented free energy table. These thermodynamic
parameters (free Gibbs energy) have been estimated using a in silico
approach and therefore lack high resolution.
    ]]></help>
    
    <citations>
        <citation type="bibtex">
           @mastersthesis{mastersthesis,