Mercurial > repos > xuebing > sharplabtool

annotate tools/emboss_5/emboss_einverted.xml @ 0:9071e359b9a3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
1 <tool id="EMBOSS: einverted28" name="einverted" version="5.0.0">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
2 <description>Finds DNA inverted repeats</description>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
4 <command>einverted -sequence $input1 -outfile $out_file1 -gap $gap -threshold $threshold -match $match -mismatch $mismatch -maxrepeat $maxrepeat -auto</command>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
5 <inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
6 <param format="fasta" name="input1" type="data">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
7 <label>On query</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
8 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
9 <param name="gap" size="4" type="text" value="12">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
10 <label>Gap penalty</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
11 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
12 <param name="threshold" size="4" type="text" value="50">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
13 <label>Minimum score threshold</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
14 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
15 <param name="match" size="4" type="text" value="3">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
16 <label>Match score</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
17 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
18 <param name="mismatch" size="4" type="text" value="-4">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
19 <label>Mismatch score</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
20 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
21 <param name="maxrepeat" size="4" type="text" value="2000">
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
22 <label>Maximum separation between the start of repeat and the end of the inverted repeat</label>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
23 </param>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
24 </inputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
25 <outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
26 <data format="einverted" name="out_file1" />
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
27 </outputs>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
28 <tests>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
29 <test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
30 <param name="input1" value="1.fasta"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
31 <param name="gap" value="12"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
32 <param name="threshold" value="50"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
33 <param name="match" value="3"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
34 <param name="mismatch" value="-4"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
35 <param name="maxrepeat" value="2000"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
36 <output name="out_file1" file="emboss_einverted_out.einverted"/>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
37 </test>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
38 </tests>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
39 <help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
40 .. class:: warningmark
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
41
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
42 The input dataset needs to be sequences.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
43
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
44 -----
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
45
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
46 You can view the original documentation here_.
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
47
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
48 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/einverted.html
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
49 </help>
9071e359b9a3 Uploaded
xuebing
parents:
diff changeset
50 </tool>