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comparison emboss_epestfind.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0.1">
2 <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' epestfind -sequence '$input1' -goutfile '$ofile2' -outfile '$ofile1' -window $window -order $order -potential $potential -poor $poor
8 -invalid $invalid -map $map -graph png -auto</command>
9 <inputs>
10 <param name="input1" type="data" format="data" label="Sequence" />
11 <param name="window" type="integer" value="10" label="Minimal distance between positively charged amino acids" />
12 <param name="order" type="select" label="Sort by">
13 <option value="3">Score</option>
14 <option value="1">Length</option>
15 <option value="2">Position</option>
16 </param>
17 <param name="threshold" type="float" value="5.0" label="Threshold value to discriminate weak from potential PEST motifs" />
18 <param name="potential" type="select" label="Decide whether potential PEST motifs should be printed">
19 <option value="yes">Yes</option>
20 <option value="no">No</option>
21 </param>
22 <param name="poor" type="select" label="Decide whether poor PEST motifs should be printed">
23 <option value="yes">Yes</option>
24 <option value="no">No</option>
25 </param>
26 <param name="invalid" type="select" label="Decide whether invalid PEST motifs should be printed">
27 <option value="no">No</option>
28 <option value="yes">Yes</option>
29 </param>
30 <param name="map" type="select" label="Decide whether PEST motifs should be mapped to sequence">
31 <option value="yes">Yes</option>
32 <option value="no">No</option>
33 </param>
34 </inputs>
35 <outputs>
36 <data name="ofile2" format="png" />
37 <data name="ofile1" format="epestfind" />
38 </outputs>
39 <!-- <tests>
40 <test>
41 <param name="input1" value="2.fasta"/>
42 <param name="window" value="10"/>
43 <param name="order" value="3"/>
44 <param name="threshold" value="5.0"/>
45 <param name="potential" value="yes"/>
46 <param name="poor" value="yes"/>
47 <param name="invalid" value="no"/>
48 <param name="map" value="yes"/>
49 <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
50 </test>
51 </tests> output file contains file location info -->
52 <help>
53 You can view the original documentation here_.
54
55 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/epestfind.html
56 </help>
57 <expand macro="citations" />
58 </tool>