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comparison tools/mummer/mummer.xml @ 4:5f5a358b281f draft

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v0.0.5 internal changes
author peterjc
date Wed, 05 Aug 2015 11:34:31 -0400
parents 154c000d3fef
children 683ea5ab0008
comparison
equal deleted inserted replaced
3:154c000d3fef 4:5f5a358b281f
1 <tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.4"> 1 <tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.5">
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>
12 <requirement type="package" version="3.23">mummer</requirement> 12 <requirement type="package" version="3.23">mummer</requirement>
13 <!-- mummerplot needs the gnuplot binary --> 13 <!-- mummerplot needs the gnuplot binary -->
14 <requirement type="binary">gnuplot</requirement> 14 <requirement type="binary">gnuplot</requirement>
15 <requirement type="package" version="4.6">gnuplot</requirement> 15 <requirement type="package" version="4.6">gnuplot</requirement>
16 </requirements> 16 </requirements>
17 <stdio>
18 <!-- Anything other than zero is an error -->
19 <exit_code range="1:" />
20 <exit_code range=":-1" />
21 </stdio>
17 <version_command interpreter="python"> 22 <version_command interpreter="python">
18 mummer.py --version 23 mummer.py --version
19 </version_command> 24 </version_command>
20 <command interpreter="python"> 25 <command interpreter="python">
21 mummer.py "$fasta_a" "$fasta_b" $algorithm "$png_output" "$pdf_output" 26 mummer.py "$fasta_a" "$fasta_b" $algorithm "$png_output" "$pdf_output"
22 </command> 27 </command>
23 <stdio>
24 <!-- Anything other than zero is an error -->
25 <exit_code range="1:" />
26 <exit_code range=":-1" />
27 </stdio>
28 <inputs> 28 <inputs>
29 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> 29 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->
30 <param name="fasta_a" type="data" format="fasta" 30 <param name="fasta_a" type="data" format="fasta"
31 label="Species A" 31 label="Species A"
32 description="Nucleotide FASTA file, e.g. contigs from genome assembly." /> 32 description="Nucleotide FASTA file, e.g. contigs from genome assembly." />
42 </inputs> 42 </inputs>
43 <outputs> 43 <outputs>
44 <data name="pdf_output" format="pdf" label="$algorithm.value PDF: $fasta_a.name vs $fasta_b.name" /> 44 <data name="pdf_output" format="pdf" label="$algorithm.value PDF: $fasta_a.name vs $fasta_b.name" />
45 <data name="png_output" format="png" label="$algorithm.value PNG: $fasta_a.name vs $fasta_b.name" /> 45 <data name="png_output" format="png" label="$algorithm.value PNG: $fasta_a.name vs $fasta_b.name" />
46 </outputs> 46 </outputs>
47 <requirements>
48 </requirements>
49 <tests> 47 <tests>
50 <!-- Because exact graphical output is fragile w.r.t. dependency versions, 48 <!-- 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. 49 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. --> 50 Rather than genomes, for size + speed just comparing 3 and 6 genes. -->
53 <test> 51 <test>
62 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" /> 60 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" />
63 <param name="algorithm" value="nucmer" /> 61 <param name="algorithm" value="nucmer" />
64 <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" /> 62 <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" />
65 <output name="png_output" file="magic.png" ftype="png" compare="contains" /> 63 <output name="png_output" file="magic.png" ftype="png" compare="contains" />
66 </test> 64 </test>
65 <!-- Commenting out as this triggers some unexplained failure on TravisCI
66 See http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-October/020764.html
67 <test> 67 <test>
68 <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta" /> 68 <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta" />
69 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" /> 69 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta" />
70 <param name="algorithm" value="promer" /> 70 <param name="algorithm" value="promer" />
71 <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" /> 71 <output name="pdf_output" file="magic.pdf" ftype="pdf" compare="contains" />
72 <output name="png_output" file="magic.png" ftype="png" compare="contains" /> 72 <output name="png_output" file="magic.png" ftype="png" compare="contains" />
73 </test> 73 </test>
74 -->
74 </tests> 75 </tests>
75 <help> 76 <help>
76 **What it does** 77 **What it does**
77 78
78 Takes two FASTA files (*species A* and *species B*), compares them using one 79 Takes two FASTA files (*species A* and *species B*), compares them using one