comparison segmentation-fold.xml @ 2:eccb5ee89df7 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit b37cb65736e2a6e76b94a9fa12a5887046437e36-dirty

1:9827a554e52f

<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"
                -f $input.input_fasta
            #else
                -s $input.input_sequence
            #end if
            
            -p $predict_segments
            -h $min_hairpin_size
            

                -x "${SEGMENTATION_FOLD_DEFAULT_XML}"
            #else
                -x $parameters.input_xml
            #end if
            
            -t \${GALAXY_SLOTS:-2}
            > $output_dbn
    ]]></command>
    
    <inputs>
        

    
    <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,

2:eccb5ee89df7

<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"
                -f $input.input_fasta
            #else
                -s ${input.input_sequence}
            #end if
            
            -p $predict_segments
            -h $min_hairpin_size
            

                -x "${SEGMENTATION_FOLD_DEFAULT_XML}"
            #else
                -x $parameters.input_xml
            #end if
            
            -t \${GALAXY_SLOTS:-4}
            > $output_dbn
    ]]></command>
    
    <inputs>
        

    
    <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,