annotate rnaplot.xml @ 2:5e58cbf27a05 draft

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<tool id="rnaplot" name="RNAplot" version="2.1.6.0">
    <description> Draw RNA Secondary Structures </description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <expand macro="stdio" />
    <macros>
        <token name="@EXECUTABLE@">RNAplot</token>
        <import>macros.xml</import>
    </macros>
    <command>
<![CDATA[
        RNAplot < $input
        --layout-type=$layoutSelector
        --output-format=$formatOptions.formatSelector
        #if str($formatOptions.formatSelector) == "ps"
            --pre=$formatOptions.pre
            --post=$formatOptions.post
            ; tar -cf $imagesFile *.ps
        #elif str($formatOptions.formatSelector) == "gml"
            ; tar -cf $imagesFile *.gml
        #elif str($formatOptions.formatSelector) == "svg"
            ; tar -cf $imagesFile *.svg
        #else
            ; tar -cf $imagesFile *.ss
        #end if
]]>
    </command>
    <inputs>
        <param format="txt" name="input" type="data" label="Fasta file"/>
        <param name="layoutSelector" type="select" label="Layout selection">
            <option value="0">Radial Layout</option>
            <option value="1" selected="true">Naview Layout</option>
        </param>
        <conditional name="formatOptions">
            <param name="formatSelector" type="select" label="Output format selection" help="--output-format">
                <option value="ps" selected="true">Postscript (.ps)</option>
                <option value="gml">Graph Meta Language (.gml)</option>
                <option value="svg">Scalable Vector Graphics (.svg)</option>
                <option value="xrna">XRNA Save File (.ss)</option>
            </param>
            <when value="ps">
                <param name="pre" size="200" type="text" label="Add annotation macros to postscript file" help="--pre"/>
                <param name="post" size="200" type="text" label="Add annotations to postscript file" help="--post"/>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="tar" name="imagesFile"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="rnaplot_input1.fas"/>
            <output name="imagesFile">
                <assert_contents>
                    <has_line line="%%Title: RNA Secondary Structure Plot"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[

**RNAplot**

The program reads RNA sequences and structures in the format as produced by RNAfold and produces drawings of the secondary structure graph. The coordinates are produced using either E. Bruccoleri's naview routines, or a simple radial layout method.

-----

**Input format**

RNAplot requires one input file

- Fasta file with an additional line with structure information in dot-bracket notation

------

**Outputs**

- several possible postscript images bundled together in a tar file


]]>
    </help>
    <expand macro="requirements" />
</tool>