Mercurial > repos > devteam > emboss_5

comparison emboss_splitter.xml @ 10:9b98d3d903c6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children 0e2484b6829b
comparison
equal deleted inserted replaced
9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: splitter92" name="splitter" version="5.0.0">
2 <description>Split a sequence into (overlapping) smaller sequences</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>splitter -sequence $input1 -outseq $out_file1 -size "$size" -overlap "$overlap" -addoverlap $addoverlap -osformat2 $out_format1 -auto</command>
5 <inputs>
6 <param format="fasta" name="input1" type="data">
7 <label>Sequences</label>
8 </param>
9 <param name="size" type="text" value="10000">
10 <label>Size to split at</label>
11 </param>
12 <param name="overlap" type="text" value="0">
13 <label>Overlap between split sequences</label>
14 </param>
15 <param name="addoverlap" type="select">
16 <label>Add overlap to size</label>
17 <option value="no">No</option>
18 <option value="yes">Yes</option>
19 </param>
20 <param name="out_format1" type="select">
21 <label>Output Sequence File Format</label>
22 <option value="fasta">FASTA (m)</option>
23 <option value="acedb">ACeDB (m)</option>
24 <option value="asn1">ASN.1 (m)</option>
25 <option value="clustal">Clustal (m)</option>
26 <option value="codata">CODATA (m)</option>
27 <option value="embl">EMBL (m)</option>
28 <option value="fitch">Fitch (m)</option>
29 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
30 <option value="genbank">GENBANK (m)</option>
31 <option value="gff">GFF (m)</option>
32 <option value="hennig86">Hennig86 (m)</option>
33 <option value="ig">Intelligenetics (m)</option>
34 <option value="jackknifer">Jackknifer (m)</option>
35 <option value="jackknifernon">Jackknifernon (m)</option>
36 <option value="mega">Mega (m)</option>
37 <option value="meganon">Meganon (m)</option>
38 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
39 <option value="pir">NBRF (PIR) (m)</option>
40 <option value="ncbi">NCBI style FASTA (m)</option>
41 <option value="nexus">Nexus/PAUP (m)</option>
42 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
43 <option value="phylip">PHYLIP interleaved (m)</option>
44 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
45 <option value="selex">SELEX (m)</option>
46 <option value="staden">Staden (s)</option>
47 <option value="strider">DNA strider (m)</option>
48 <option value="swiss">SwisProt entry (m)</option>
49 <option value="text">Plain sequence (s)</option>
50 <option value="treecon">Treecon (m)</option>
51 </param>
52 </inputs>
53 <outputs>
54 <data format="fasta" name="out_file1" />
55 </outputs>
56 <tests>
57 <test>
58 <param name="input1" value="2.fasta"/>
59 <param name="size" value="10000"/>
60 <param name="overlap" value="0"/>
61 <param name="addoverlap" value="no"/>
62 <param name="out_format1" value="fasta"/>
63 <output name="out_file1" file="emboss_splitter_out.fasta"/>
64 </test>
65 </tests>
66 <code file="emboss_format_corrector.py" />
67 <help>
68
69 .. class:: warningmark
70
71 The input dataset needs to be sequences.
72
73 -----
74
75 You can view the original documentation here_.
76
77 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/splitter.html
78
79 ------
80
81 **Citation**
82
83 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;`_
84
85 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;`_
86 </help>
87 </tool>