Mercurial > repos > peterjc > mummer
view tools/mummer/mummer.xml @ 5:683ea5ab0008 draft
v0.0.6 Fixed input parameter help text
author | peterjc |
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date | Wed, 01 Feb 2017 06:58:01 -0500 |
parents | 5f5a358b281f |
children | d9f3d4779507 |
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<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>