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/tools/emboss_5/emboss_palindrome.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 59 lines | 51 code | 8 blank | 0 comment | 0 complexity | 617a1139c05426a24cd880ff482c92c6 MD5 | raw file
 1<tool id="EMBOSS: palindrome65" name="palindrome" version="5.0.0">
 2  <description>Looks for inverted repeats in a nucleotide sequence</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>palindrome -sequence $input1 -outfile $out_file1 -minpallen $minpallen -maxpallen $maxpallen -gaplimit $gaplimit -nummismatches $nummismatches -overlap $overlap -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>Sequences</label>
 8    </param>
 9    <param name="minpallen" size="4" type="text" value="10">
10      <label>Minimum length of palindrome</label>
11    </param>
12    <param name="maxpallen" size="4" type="text" value="100">
13      <label>Maximum length of palindrome</label>
14    </param>
15    <param name="gaplimit" size="4" type="text" value="100">
16      <label>Maximum gap between repeated regions</label>
17    </param>
18    <param name="nummismatches" size="4" type="text" value="0">
19      <label>Number of mismatches allowed</label>
20    </param>
21    <param name="overlap" type="select">
22      <label>Report overlapping matches</label>
23      <option value="yes">Yes</option>
24      <option value="no">No</option>
25    </param>
26  </inputs>
27  <outputs>
28    <data format="palindrome" name="out_file1" />
29  </outputs>
30  <tests>
31    <test>
32      <param name="input1" value="2.fasta"/>
33      <param name="minpallen" value="10"/>
34      <param name="maxpallen" value="100"/>
35      <param name="gaplimit" value="100"/>
36      <param name="nummismatches" value="0"/>
37      <param name="overlap" value="yes"/>
38      <output name="out_file1" file="emboss_palindrome_out.palindrome"/>
39    </test>
40  </tests>
41  <help>
42
43.. class:: warningmark
44
45The input dataset needs to be sequences.
46
47-----
48
49    You can view the original documentation here_.
50    
51    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/palindrome.html
52
53------
54
55**Citation**
56
57If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
58  </help>
59</tool>