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/tools/emboss_5/emboss_prettyseq.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="EMBOSS: prettyseq80" name="prettyseq" version="5.0.0">
 2  <description>Output sequence with translated ranges</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>prettyseq -sequence $input1 -outfile $out_file1 -ruler $ruler -plabel $plabel -nlabel $nlabel -width $width -auto</command>
 5  <inputs>
 6    <param format="fasta" name="input1" type="data">
 7      <label>Sequence</label>
 8    </param>
 9    <param name="ruler" type="select">
10      <label>Add a ruler</label>
11      <option value="yes">Yes</option>
12      <option value="no">No</option>
13    </param>
14    <param name="plabel" type="select">
15      <label>Number translations</label>
16      <option value="yes">Yes</option>
17      <option value="no">No</option>
18    </param>
19    <param name="nlabel" type="select">
20      <label>Number DNA sequence</label>
21      <option value="yes">Yes</option>
22      <option value="no">No</option>
23    </param>
24    <param name="width" size="4" type="text" value="60">
25      <label>Width of screen</label>
26    </param>
27  </inputs>
28  <outputs>
29    <data format="prettyseq" name="out_file1" />
30  </outputs>
31  <tests>
32    <test>
33      <param name="input1" value="2.fasta"/>
34      <param name="ruler" value="yes"/>
35      <param name="plabel" value="yes"/>
36      <param name="nlabel" value="yes"/>
37      <param name="width" value="60"/>
38      <output name="out_file1" file="emboss_prettyseq_out.prettyseq"/>
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/prettyseq.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>