Mercurial > repos > peterjc > mummer
diff tools/mummer/mummer.xml @ 3:154c000d3fef draft
Uploaded v0.0.4 with test case and ToolShed dependency for gnuplot
author | peterjc |
---|---|
date | Thu, 06 Nov 2014 11:50:19 -0500 |
parents | 8f93c1b7609e |
children | 5f5a358b281f |
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--- a/tools/mummer/mummer.xml Tue Oct 28 09:43:52 2014 -0400 +++ b/tools/mummer/mummer.xml Thu Nov 06 11:50:19 2014 -0500 @@ -1,4 +1,4 @@ -<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.3"> +<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.4"> <description>Combine mummer/nucmer/promer with mummerplot</description> <requirements> <!-- Needs ps2pdf from ghostscript --> @@ -10,6 +10,9 @@ <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> <version_command interpreter="python"> mummer.py --version @@ -44,6 +47,30 @@ <requirements> </requirements> <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> + <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**