root/galaxy-central/tools/emboss_5/emboss_einverted.xml

リビジョン 2, 1.8 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
2  <description>Finds DNA inverted repeats</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
5  <inputs>
6    <param format="fasta" name="input1" type="data">
7      <label>On query</label>
8    </param>
9    <param name="gap" size="4" type="text" value="12">
10      <label>Gap penalty</label>
11    </param>
12    <param name="threshold" size="4" type="text" value="50">
13      <label>Minimum score threshold</label>
14    </param>
15    <param name="match" size="4" type="text" value="3">
16      <label>Match score</label>
17    </param>
18    <param name="mismatch" size="4" type="text" value="-4">
19      <label>Mismatch score</label>
20    </param>
21    <param name="maxrepeat" size="4" type="text" value="2000">
22      <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
23    </param>
24  </inputs>
25  <outputs>
26    <data format="einverted" name="out_file1" />
27  </outputs>
28  <tests>
29    <test>
30      <param name="input1" value="1.fasta"/>
31      <param name="gap" value="12"/>
32      <param name="threshold" value="50"/>
33      <param name="match" value="3"/>
34      <param name="mismatch" value="-4"/>
35      <param name="maxrepeat" value="2000"/>
36      <output name="out_file1" file="emboss_einverted_out.einverted"/>
37    </test>
38  </tests>
39  <help>
40.. class:: warningmark
41
42The input dataset needs to be sequences.
43
44-----
45
46    You can view the original documentation here_.
47   
48    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html
49  </help>
50</tool>
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