root/galaxy-central/tools/emboss_5/emboss_epestfind.xml @ 3

リビジョン 2, 2.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: epestfind29" name="epestfind" version="5.0.0">
2  <description>Finds PEST motifs as potential proteolytic cleavage sites</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command interpreter="perl">emboss_single_outputfile_wrapper.pl epestfind -sequence $input1 -goutfile $ofile2 -outfile $ofile1 -window $window -order $order -potential $potential -poor $poor
5  -invalid $invalid -map $map -graph png -auto</command>
6  <inputs>
7    <param format="data" name="input1" type="data">
8      <label>Sequence</label>
9    </param>
10    <param name="window" size="4" type="text" value="10">
11      <label>Minimal distance between positively charged amino acids</label>
12    </param>
13    <param name="order" type="select">
14      <label>Sort by</label>
15      <option value="3">Score</option>
16      <option value="1">Length</option>
17      <option value="2">Position</option>
18    </param>
19    <param name="threshold" size="4" type="text" value="5.0">
20      <label>Threshold value to discriminate weak from potential PEST motifs.</label>
21    </param>
22    <param name="potential" type="select">
23      <label>Decide whether potential PEST motifs should be printed</label>
24      <option value="yes">Yes</option>
25      <option value="no">No</option>
26    </param>
27    <param name="poor" type="select">
28      <label>Decide whether poor PEST motifs should be printed</label>
29      <option value="yes">Yes</option>
30      <option value="no">No</option>
31    </param>
32    <param name="invalid" type="select">
33      <label>Decide whether invalid PEST motifs should be printed</label>
34      <option value="no">No</option>
35      <option value="yes">Yes</option>
36    </param>
37    <param name="map" type="select">
38      <label>Decide whether PEST motifs should be mapped to sequence</label>
39      <option value="yes">Yes</option>
40      <option value="no">No</option>
41    </param>
42  </inputs>
43  <outputs>
44    <data format="png" name="ofile2" />
45    <data format="epestfind" name="ofile1" />
46  </outputs>
47<!--    <tests>
48    <test>
49      <param name="input1" value="2.fasta"/>
50      <param name="window" value="10"/>
51      <param name="order" value="3"/>
52      <param name="threshold" value="5.0"/>
53      <param name="potential" value="yes"/>
54      <param name="poor" value="yes"/>
55      <param name="invalid" value="no"/>
56      <param name="map" value="yes"/>
57      <output name="ofile1" file="emboss_epestfind_out.epestfind"/>
58    </test>
59  </tests>  output file contains file location info  -->
60  <help>
61    You can view the original documentation here_.
62   
63    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/epestfind.html
64  </help>
65</tool>
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