Mercurial > repos > devteam > emboss_5
comparison emboss_palindrome.xml @ 10:d49956b87f7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author | iuc |
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date | Wed, 08 Feb 2017 12:42:22 -0500 |
parents | |
children | 8992d258e42f |
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9:511429456d3c | 10:d49956b87f7e |
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1 <tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0.1"> | |
2 <description>Looks for inverted repeats in a nucleotide sequence</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command>palindrome -sequence '$input1' -outfile '$out_file1' -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command> | |
8 <inputs> | |
9 <param name="input1" type="data" format="fasta" label="Sequences" /> | |
10 <param name="minpallen" type="integer" value="10" label="Minimum length of palindrome" /> | |
11 <param name="maxpallen" type="integer" value="100" label="Maximum length of palindrome" /> | |
12 <param name="gaplimit" type="integer" value="100" label="Maximum gap between repeated regions" /> | |
13 <param name="nummismatches" type="integer" value="0" label="Number of mismatches allowed" /> | |
14 <param name="overlap" type="select" label="Report overlapping matches"> | |
15 <option value="yes">Yes</option> | |
16 <option value="no">No</option> | |
17 </param> | |
18 </inputs> | |
19 <outputs> | |
20 <data name="out_file1" format="palindrome" /> | |
21 </outputs> | |
22 <tests> | |
23 <test> | |
24 <param name="input1" value="2.fasta"/> | |
25 <param name="minpallen" value="10"/> | |
26 <param name="maxpallen" value="100"/> | |
27 <param name="gaplimit" value="100"/> | |
28 <param name="nummismatches" value="0"/> | |
29 <param name="overlap" value="yes"/> | |
30 <output name="out_file1" file="emboss_palindrome_out.palindrome"/> | |
31 </test> | |
32 </tests> | |
33 <help> | |
34 .. class:: warningmark | |
35 | |
36 The input dataset needs to be sequences. | |
37 | |
38 ----- | |
39 | |
40 You can view the original documentation here_. | |
41 | |
42 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/palindrome.html | |
43 </help> | |
44 <expand macro="citations" /> | |
45 </tool> |