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comparison emboss_einverted.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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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
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>