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comparison emboss_shuffleseq.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: shuffleseq87" name="shuffleseq" version="5.0.0">
2 <!-- produces random outputs each time -->
3 <description>Shuffles a set of sequences maintaining composition</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
5 <command>shuffleseq -sequence $input1 -outseq $out_file1 -shuffle "$shuffle" -osformat2 $out_format1 -auto</command>
6 <inputs>
7 <param format="fasta" name="input1" type="data">
8 <label>Sequences</label>
9 </param>
10 <param name="shuffle" type="text" value="1">
11 <label>Number of shuffles</label>
12 </param>
13 <param name="out_format1" type="select">
14 <label>Output Sequence File Format</label>
15 <option value="fasta">FASTA (m)</option>
16 <option value="acedb">ACeDB (m)</option>
17 <option value="asn1">ASN.1 (m)</option>
18 <option value="clustal">Clustal (m)</option>
19 <option value="codata">CODATA (m)</option>
20 <option value="embl">EMBL (m)</option>
21 <option value="fitch">Fitch (m)</option>
22 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
23 <option value="genbank">GENBANK (m)</option>
24 <option value="gff">GFF (m)</option>
25 <option value="hennig86">Hennig86 (m)</option>
26 <option value="ig">Intelligenetics (m)</option>
27 <option value="jackknifer">Jackknifer (m)</option>
28 <option value="jackknifernon">Jackknifernon (m)</option>
29 <option value="mega">Mega (m)</option>
30 <option value="meganon">Meganon (m)</option>
31 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
32 <option value="pir">NBRF (PIR) (m)</option>
33 <option value="ncbi">NCBI style FASTA (m)</option>
34 <option value="nexus">Nexus/PAUP (m)</option>
35 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
36 <option value="phylip">PHYLIP interleaved (m)</option>
37 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
38 <option value="selex">SELEX (m)</option>
39 <option value="staden">Staden (s)</option>
40 <option value="strider">DNA strider (m)</option>
41 <option value="swiss">SwisProt entry (m)</option>
42 <option value="text">Plain sequence (s)</option>
43 <option value="treecon">Treecon (m)</option>
44 </param>
45 </inputs>
46 <outputs>
47 <data format="fasta" name="out_file1" />
48 </outputs>
49 <code file="emboss_format_corrector.py" />
50 <help>
51
52 .. class:: warningmark
53
54 The input dataset needs to be sequences.
55
56 -----
57
58 You can view the original documentation here_.
59
60 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/shuffleseq.html
61
62 ------
63
64 **Citation**
65
66 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;`_
67
68 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;`_
69 </help>
70 </tool>