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> |
---|