Mercurial > repos > devteam > emboss_5
comparison emboss_einverted.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: einverted28" name="einverted" version="5.0.0.1"> | |
2 <description>Finds DNA inverted repeats</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command>einverted -sequence '$input1' -outfile '$out_file1' -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command> | |
8 <inputs> | |
9 <param name="input1" type="data" format="fasta" label="On query" /> | |
10 <param name="gap" type="integer" value="12" label="Gap penalty" /> | |
11 <param name="threshold" type="integer" value="50" label="Minimum score threshold" /> | |
12 <param name="match" type="integer" value="3" label="Match score" /> | |
13 <param name="mismatch" type="integer" value="-4" label="Mismatch score" /> | |
14 <param name="maxrepeat" type="integer" value="2000" label="Maximum separation between the start of repeat and the end of the inverted repeat" /> | |
15 </inputs> | |
16 <outputs> | |
17 <data name="out_file1" format="einverted" /> | |
18 </outputs> | |
19 <tests> | |
20 <test> | |
21 <param name="input1" value="1.fasta"/> | |
22 <param name="gap" value="12"/> | |
23 <param name="threshold" value="50"/> | |
24 <param name="match" value="3"/> | |
25 <param name="mismatch" value="-4"/> | |
26 <param name="maxrepeat" value="2000"/> | |
27 <output name="out_file1" file="emboss_einverted_out.einverted"/> | |
28 </test> | |
29 </tests> | |
30 <help> | |
31 .. class:: warningmark | |
32 | |
33 The input dataset needs to be sequences. | |
34 | |
35 ----- | |
36 | |
37 You can view the original documentation here_. | |
38 | |
39 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/einverted.html | |
40 </help> | |
41 <expand macro="citations" /> | |
42 </tool> |