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/tools/emboss_5/emboss_diffseq.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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 1<tool id="EMBOSS: diffseq22" name="diffseq" version="5.0.0">
 2  <description>Find differences between nearly identical sequences</description>
 3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
 4  <command>diffseq -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize $wordsize -globaldifferences $globaldifferences -rformat3
 5  $out_format1 -offormat4 $out_format2 -offormat5 $out_format3 -auto</command>
 6  <inputs>
 7    <param format="data" name="input1" type="data">
 8      <label>Sequence 1</label>
 9    </param>
10    <param format="data" name="input2" type="data">
11      <label>Sequence 2</label>
12    </param>
13    <param name="wordsize" size="4" type="text" value="20">
14      <label>Wordsize</label>
15    </param>
16    <param name="globaldifferences" type="select">
17      <label>Report differences at the ends</label>
18      <option value="no">No</option>
19      <option value="yes">Yes</option>
20    </param>
21    <param name="out_format1" type="select">
22      <label>Output Report File Format</label>
23      <option value="diffseq">Diffseq</option>
24      <option value="embl">EMBL</option>
25      <option value="genbank">GENBANK</option>
26      <option value="gff">GFF</option>
27      <option value="pir">PIR</option>
28      <option value="swiss">SwissProt</option>
29      <option value="dbmotif">DbMotif</option>
30      <option value="excel">Excel (tab delimited)</option>
31      <option value="feattable">FeatTable</option>
32      <option value="motif">Motif</option>
33      <option value="regions">Regions</option>
34      <option value="seqtable">SeqTable</option>
35      <option value="simple">SRS Simple</option>
36      <option value="srs">SRS</option>
37      <option value="table">Table</option>
38      <option value="tagseq">TagSeq</option>
39    </param>
40    <param name="out_format2" type="select">
41      <label>Sequence 1 Output Feature File Format</label>
42      <option value="gff">GFF</option>
43      <option value="embl">EMBL</option>
44      <option value="swiss">SwissProt</option>
45    </param>
46    <param name="out_format3" type="select">
47      <label>Sequence 2 Output Feature File Format</label>
48      <option value="gff">GFF</option>
49      <option value="embl">EMBL</option>
50      <option value="swiss">SwissProt</option>
51    </param>
52  </inputs>
53  <outputs>
54    <data format="diffseq" name="out_file1" />
55    <data format="gff" name="out_file2" />
56    <data format="gff" name="out_file3" />
57  </outputs>
58  <code file="emboss_format_corrector.py" />
59  <help>
60    You can view the original documentation here_.
61    
62    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/diffseq.html
63
64------
65
66**Citation**
67
68If 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;`_
69  </help>
70</tool>