comparison segmentation-fold.xml @ 6:4d16cf9414cf draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/segmentation_fold commit 3a3c1d069e0a079d8ea7c0b4ac856ef24141b1aa

5:b7cf9b172cfe

    <description>RNA-Folding including predefined segments including K-turns</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    
    <requirements>
        <requirement type="package" version="1.6.5">segmentation-fold</requirement>
    </requirements>
    
    <expand macro="stdio" />
    
    <version_command>@VERSION_COMMAND_SMF@</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
            
            #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 value="fasta">
                <param name="input_fasta" type="data" format="fasta" label="Fasta file with RNA-sequece (-f)" />
            </when>
            <when value="text"> 
                <param name="input_sequence" type="text" label="RNA-sequece (-s)" />
            </when>
        </conditional>
        
        <param name="predict_segments" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Enable segment prediction functionality (-p)" />
        <param name="min_hairpin_size" type="integer" min="1" value="3" label="Minimum hairpin size (-h)" />
        
        <conditional name="parameters">
            <param name="settings" type="select" label="Energy parameters">
                <option value="default" selected="true">Default</option>
                <option value="custom">Custom</option>
            </param>
            <when value="default" />
            <when value="custom"> 
                <param name="input_xml" type="data" format="xml" multiple="false" label="Use custom 'segments.xml'-syntaxed file (-x)" />
            </when>
        </conditional>
    </inputs>
    
    <outputs>

https://wiki.galaxyproject.org/Learn/Datatypes#Dbn

**Authors**

Youri Hoogstrate (yhoogstrate @ github)
    ]]></help>
    
    <expand macro="citations" />
</tool>

6:4d16cf9414cf

    <description>RNA-Folding including predefined segments including K-turns</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    
    <expand macro="requirements" />
    <expand macro="version_command" />
    
    <command detect_errors="aggressive"><![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
            
            #if $parameters.settings == "custom"
                -x '${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 value="fasta">
                <param name="input_fasta" type="data" format="fasta" label="Fasta file with RNA-sequece" argument="-f" />
            </when>
            <when value="text"> 
                <param name="input_sequence" type="text" label="RNA-sequence" argument="-s" />
            </when>
        </conditional>
        
        <param name="predict_segments" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Enable segment prediction functionality" argument="-p" />
        <param name="min_hairpin_size" type="integer" min="1" value="3" label="Minimum hairpin size" argument="-h" />
        
        <conditional name="parameters">
            <param name="settings" type="select" label="Energy parameters">
                <option value="default" selected="true">Default</option>
                <option value="custom">Custom</option>
            </param>
            <when value="default" />
            <when value="custom"> 
                <param name="input_xml" type="data" format="xml" multiple="false" label="Use custom 'segments.xml'-syntaxed file" argument="-x" />
            </when>
        </conditional>
    </inputs>
    
    <outputs>

https://wiki.galaxyproject.org/Learn/Datatypes#Dbn

**Authors**

Youri Hoogstrate (GitHub: @yhoogstrate)
    ]]></help>
    
    <expand macro="citations" />
</tool>