Mercurial > repos > peterjc > mummer
diff tools/mummer/mummer.xml @ 0:b0551f2a5986 draft
Uploaded v0.0.1, essentially a preview (previously only on the TestToolShed). No tests yet, no gnuplot or ps2pdf dependency yet.
author | peterjc |
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date | Mon, 27 Oct 2014 12:56:55 -0400 |
parents | |
children | b07aa90c95e6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mummer/mummer.xml Mon Oct 27 12:56:55 2014 -0400 @@ -0,0 +1,68 @@ +<tool id="mumer_wrapper" name="MUMmer" version="0.0.1"> + <description>Draw dotplot with mummer/nucmer/promer/mummerplot</description> + <requirements> + <requirement type="binary">ps2pdf</requirement> + <requirement type="binary">nucmer</requirement> + <requirement type="binary">mummerplot</requirement> + <requirement type="package" version="3.23">mummer</requirement> + </requirements> + <version_command interpreter="python"> +mummer.py --version + </version_command> + <command interpreter="python"> +mummer.py "$fasta_a" "$fasta_b" $algorithm "$png_output" "$pdf_output" + </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <inputs> + <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> + <param name="fasta_a" type="data" format="fasta" + label="Species A" + description="Nucleotide FASTA file, e.g. contigs from genome assembly." /> + <param name="fasta_b" type="data" format="fasta" + label="Species B" + description="Nucleotide FASTA file, e.g. contigs from genome assembly." /> + <param name="algorithm" type="select" label="MUMmer search algorithm"> + <option value="mummer">mummer, efficiently locates maximal unique matches between two sequences</option> + <option value="nucmer">NUCmer (NUCleotide MUMmer), for closely related sequences</option> + <option value="promer">PROmer (PROtein MUMmer), using six frame translation of DNA input, for less similar sequences.</option> + </param> + <!-- defaults like mincluster vary, 65 for nucmer but 20 for promer --> + </inputs> + <outputs> + <data name="pdf_output" format="pdf" label="$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> + <requirements> + </requirements> + <tests> + </tests> + <help> +**What it does** + +Takes two FASTA files (*species A* and *species B*), compairs them using one +of the MUMmer 3 tools (``mummer``, ``nucmer``, or ``promer``), comparing 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> +</tool>