annotate tools/mummer/mummer.xml @ 5:683ea5ab0008 draft

v0.0.6 Fixed input parameter help text

<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.6">
    <description>Combine mummer/nucmer/promer with mummerplot</description>
    <requirements>
            <!-- Needs ps2pdf from ghostscript -->      
            <requirement type="binary">ps2pdf</requirement>
            <requirement type="package" version="9.10">ghostscript</requirement>
            <!-- Needs mummer, nucmer, promer and mummerplot from MUMmer -->
            <requirement type="binary">mummer</requirement>
            <requirement type="binary">nucmer</requirement>
            <requirement type="binary">promer</requirement>
            <requirement type="binary">mummerplot</requirement>
            <requirement type="package" version="3.23">mummer</requirement>
	    <!-- mummerplot needs the gnuplot binary -->
            <requirement type="binary">gnuplot</requirement>
            <requirement type="package" version="4.6">gnuplot</requirement>
    </requirements>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <version_command interpreter="python">
mummer.py --version
    </version_command>
    <command interpreter="python">
mummer.py "$fasta_a" "$fasta_b" $algorithm "$png_output" "$pdf_output"
    </command>
    <inputs>
        <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->
        <param name="fasta_a" type="data" format="fasta"
	       label="Species A"
	       help="Nucleotide FASTA file, e.g. contigs from genome assembly." /> 
        <param name="fasta_b" type="data" format="fasta"
	       label="Species B"
	       help="Nucleotide FASTA file, e.g. contigs from genome assembly." /> 
        <param name="algorithm" type="select" label="MUMmer search algorithm">
            <option value="mummer">mummer, efficiently locates maximal unique matches between two sequences</option>
            <option value="nucmer">NUCmer (NUCleotide MUMmer), for closely related sequences</option>
            <option value="promer">PROmer (PROtein MUMmer), using six frame translation of DNA input, for less similar sequences.</option>
        </param>
	<!-- defaults like mincluster vary, 65 for nucmer but 20 for promer -->
    </inputs>
    <outputs>
        <data name="pdf_output" format="pdf" label="$algorithm.value PDF: $fasta_a.name vs $fasta_b.name" />
        <data name="png_output" format="png" label="$algorithm.value PNG: $fasta_a.name vs $fasta_b.name" />
    </outputs>
    <tests>
        <!-- Because exact graphical output is fragile w.r.t. dependency versions,
             all I am trying to verify is a valid PNG and PDF are produced.
             Rather than genomes, for size + speed just comparing 3 and 6 genes. -->
        <test>
            <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta" />
            <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" />
            <param name="algorithm" value="mummer" />
            <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" />
            <output name="png_output" file="magic.png" ftype="png" compare="contains" />
        </test>
        <test>
            <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta" />
            <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" />
            <param name="algorithm" value="nucmer" />
            <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" />
            <output name="png_output" file="magic.png" ftype="png" compare="contains" />
        </test>
        <!-- Commenting out as this triggers some unexplained failure on TravisCI
             See http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-October/020764.html
        <test>
            <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta" />
            <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" />
            <param name="algorithm" value="promer" />
            <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" />
            <output name="png_output" file="magic.png" ftype="png" compare="contains" />
        </test>
        -->
    </tests>
    <help>
**What it does**

Takes two FASTA files (*species A* and *species B*), compares them using one
of the MUMmer 3 tools (``mummer``, ``nucmer``, or ``promer``), checking both
strands, and then draws a dotplot using ``mummerplot``.

The full MUMmer suite is more flexible and capable than this limited wrapper.

**References**

MUMmer manual: v3.22 http://mummer.sourceforge.net/manual/

MUMmer tutorials: http://mummer.sourceforge.net/examples/

If you use MUMmer 3, please cite:

S. Kurtz et al. (2004).
Versatile and open software for comparing large genomes.
Genome Biology (2004), 5:R12.
http://dx.doi.org/10.1186/gb-2004-5-2-r12

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mummer
    </help>
    <citations>
        <citation type="doi">10.1186/gb-2004-5-2-r12</citation>
    </citations>
</tool>