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comparison emboss_equicktandem.xml @ 10:9b98d3d903c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0">
2 <description>Finds tandem repeats</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
5 <inputs>
6 <param format="fasta" name="input1" type="data">
7 <label>Sequence</label>
8 </param>
9 <param name="maxrepeat" type="text" value="600">
10 <label>Maximum repeat size</label>
11 </param>
12 <param name="threshold" type="text" value="20">
13 <label>Threshold score</label>
14 </param>
15 <param name="out_format1" type="select">
16 <label>Output Report File Format</label>
17 <option value="table">Table</option>
18 <option value="embl">EMBL</option>
19 <option value="genbank">GENBANK</option>
20 <option value="gff">GFF</option>
21 <option value="pir">PIR</option>
22 <option value="swiss">SwissProt</option>
23 <option value="dbmotif">DbMotif</option>
24 <option value="diffseq">Diffseq</option>
25 <option value="excel">Excel (tab delimited)</option>
26 <option value="feattable">FeatTable</option>
27 <option value="motif">Motif</option>
28 <option value="regions">Regions</option>
29 <option value="seqtable">SeqTable</option>
30 <option value="simple">SRS Simple</option>
31 <option value="srs">SRS</option>
32 <option value="tagseq">TagSeq</option>
33 </param>
34 </inputs>
35 <outputs>
36 <data format="table" name="out_file1" />
37 <data format="equicktandem" name="ofile2" />
38 </outputs>
39 <tests>
40 <test>
41 <param name="input1" value="1.fasta"/>
42 <param name="maxrepeat" value="600"/>
43 <param name="threshold" value="20"/>
44 <param name="out_format1" value="table"/>
45 <output name="ofile2" file="emboss_equicktandem_out.equicktandem"/>
46 </test>
47 </tests>
48 <code file="emboss_format_corrector.py" />
49 <help>
50 .. class:: warningmark
51
52 The input dataset needs to be sequences.
53
54 -----
55
56 You can view the original documentation here_.
57
58 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/equicktandem.html
59
60 ------
61
62 **Citation**
63
64 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
65
66 If 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;`_
67 </help>
68 </tool>