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comparison emboss_newseq.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: newseq59" name="newseq" version="5.0.0">
2 <description>Type in a short new sequence</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command>
5 <![CDATA[
6 newseq
7 -outseq '$out_file1'
8 -name '$seqname'
9 -description '$description'
10 -type '$type'
11 -sequence '$sequence'
12 -osformat5 '$out_format1'
13 -auto
14 ]]>
15 </command>
16 <inputs>
17 <param name="seqname" type="text" value="">
18 <label>Name of of the sequence</label>
19 </param>
20 <param name="description" type="text" value="">
21 <label>Description of the sequence</label>
22 </param>
23 <param name="type" type="select">
24 <label>Type of sequence</label>
25 <option value="N">Nucleic</option>
26 <option value="P">Protein</option>
27 </param>
28 <param name="sequence" type="text" value="">
29 <label>The sequence itself</label>
30 </param>
31 <param name="out_format1" type="select">
32 <label>Output Sequence File Format</label>
33 <option value="fasta">FASTA (m)</option>
34 <option value="acedb">ACeDB (m)</option>
35 <option value="asn1">ASN.1 (m)</option>
36 <option value="clustal">Clustal (m)</option>
37 <option value="codata">CODATA (m)</option>
38 <option value="embl">EMBL (m)</option>
39 <option value="fitch">Fitch (m)</option>
40 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
41 <option value="genbank">GENBANK (m)</option>
42 <option value="gff">GFF (m)</option>
43 <option value="hennig86">Hennig86 (m)</option>
44 <option value="ig">Intelligenetics (m)</option>
45 <option value="jackknifer">Jackknifer (m)</option>
46 <option value="jackknifernon">Jackknifernon (m)</option>
47 <option value="mega">Mega (m)</option>
48 <option value="meganon">Meganon (m)</option>
49 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
50 <option value="pir">NBRF (PIR) (m)</option>
51 <option value="ncbi">NCBI style FASTA (m)</option>
52 <option value="nexus">Nexus/PAUP (m)</option>
53 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
54 <option value="phylip">PHYLIP interleaved (m)</option>
55 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
56 <option value="selex">SELEX (m)</option>
57 <option value="staden">Staden (s)</option>
58 <option value="strider">DNA strider (m)</option>
59 <option value="swiss">SwisProt entry (m)</option>
60 <option value="text">Plain sequence (s)</option>
61 <option value="treecon">Treecon (m)</option>
62 </param>
63 </inputs>
64 <outputs>
65 <data format="fasta" name="out_file1" />
66 </outputs>
67 <tests>
68 <test>
69 <param name="seqname" value="cytoc"/>
70 <param name="description" value="fragment_of_cytochrome_c"/>
71 <param name="type" value="N"/>
72 <param name="sequence" value="KKKEERADLIAY"/>
73 <param name="out_format1" value="fasta"/>
74 <output name="out_file1" file="emboss_newseq_out.fasta"/>
75 </test>
76 </tests>
77 <code file="emboss_format_corrector.py" />
78 <help>
79 You can view the original documentation here_.
80
81 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newseq.html
82
83 ------
84
85 **Citation**
86
87 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;`_
88
89 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;`_
90 </help>
91 </tool>