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comparison tools/mummer/mummer.xml @ 3:154c000d3fef draft

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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
comparison
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2:8f93c1b7609e 3:154c000d3fef
1 <tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.3"> 1 <tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.4">
2 <description>Combine mummer/nucmer/promer with mummerplot</description> 2 <description>Combine mummer/nucmer/promer with mummerplot</description>
3 <requirements> 3 <requirements>
4 <!-- Needs ps2pdf from ghostscript --> 4 <!-- Needs ps2pdf from ghostscript -->
5 <requirement type="binary">ps2pdf</requirement> 5 <requirement type="binary">ps2pdf</requirement>
6 <requirement type="package" version="9.10">ghostscript</requirement> 6 <requirement type="package" version="9.10">ghostscript</requirement>
8 <requirement type="binary">mummer</requirement> 8 <requirement type="binary">mummer</requirement>
9 <requirement type="binary">nucmer</requirement> 9 <requirement type="binary">nucmer</requirement>
10 <requirement type="binary">promer</requirement> 10 <requirement type="binary">promer</requirement>
11 <requirement type="binary">mummerplot</requirement> 11 <requirement type="binary">mummerplot</requirement>
12 <requirement type="package" version="3.23">mummer</requirement> 12 <requirement type="package" version="3.23">mummer</requirement>
13 <!-- mummerplot needs the gnuplot binary -->
14 <requirement type="binary">gnuplot</requirement>
15 <requirement type="package" version="4.6">gnuplot</requirement>
13 </requirements> 16 </requirements>
14 <version_command interpreter="python"> 17 <version_command interpreter="python">
15 mummer.py --version 18 mummer.py --version
16 </version_command> 19 </version_command>
17 <command interpreter="python"> 20 <command interpreter="python">
42 <data name="png_output" format="png" label="$algorithm.value PNG: $fasta_a.name vs $fasta_b.name" /> 45 <data name="png_output" format="png" label="$algorithm.value PNG: $fasta_a.name vs $fasta_b.name" />
43 </outputs> 46 </outputs>
44 <requirements> 47 <requirements>
45 </requirements> 48 </requirements>
46 <tests> 49 <tests>
50 <!-- Because exact graphical output is fragile w.r.t. dependency versions,
51 all I am trying to verify is a valid PNG and PDF are produced.
52 Rather than genomes, for size + speed just comparing 3 and 6 genes. -->
53 <test>
54 <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta" />
55 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" />
56 <param name="algorithm" value="mummer" />
57 <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" />
58 <output name="png_output" file="magic.png" ftype="png" compare="contains" />
59 </test>
60 <test>
61 <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta" />
62 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" />
63 <param name="algorithm" value="nucmer" />
64 <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" />
65 <output name="png_output" file="magic.png" ftype="png" compare="contains" />
66 </test>
67 <test>
68 <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta" />
69 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" />
70 <param name="algorithm" value="promer" />
71 <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" />
72 <output name="png_output" file="magic.png" ftype="png" compare="contains" />
73 </test>
47 </tests> 74 </tests>
48 <help> 75 <help>
49 **What it does** 76 **What it does**
50 77
51 Takes two FASTA files (*species A* and *species B*), compares them using one 78 Takes two FASTA files (*species A* and *species B*), compares them using one