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comparison emboss_coderet.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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children 0e2484b6829b
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9:18a63c800a4d 10:9b98d3d903c6
1 <tool id="EMBOSS: coderet13" name="coderet" version="5.0.0">
2 <description>Extract CDS, mRNA and translations from feature tables</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <!-- <command>coderet -seqall $input1 -outfile $out_file1 -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
5 <command>coderet -seqall $input1 -outfile $out_file1 -auto</command>
6 <inputs>
7 <param format="data" name="input1" type="data">
8 <label>On query</label>
9 </param>
10 <!--
11 <param name="cds" type="boolean" truevalue="yes" falsevalue="no" checked="true">
12 <label>Extract CDS sequences</label>
13 </param>
14 <param name="mrna" type="select">
15 <label>Extract mRNA sequences</label>
16 <option value="yes">Yes</option>
17 <option value="no">No</option>
18 </param>
19 <param name="translation" type="select">
20 <label>Extract translated sequences</label>
21 <option value="yes">Yes</option>
22 <option value="no">No</option>
23 </param>
24 <param name="out_format1" type="select">
25 <label>Output Sequence File Format</label>
26 <option value="fasta">FASTA (m)</option>
27 <option value="acedb">ACeDB (m)</option>
28 <option value="asn1">ASN.1 (m)</option>
29 <option value="clustal">Clustal (m)</option>
30 <option value="codata">CODATA (m)</option>
31 <option value="embl">EMBL (m)</option>
32 <option value="fitch">Fitch (m)</option>
33 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
34 <option value="genbank">GENBANK (m)</option>
35 <option value="gff">GFF (m)</option>
36 <option value="hennig86">Hennig86 (m)</option>
37 <option value="ig">Intelligenetics (m)</option>
38 <option value="jackknifer">Jackknifer (m)</option>
39 <option value="jackknifernon">Jackknifernon (m)</option>
40 <option value="mega">Mega (m)</option>
41 <option value="meganon">Meganon (m)</option>
42 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
43 <option value="pir">NBRF (PIR) (m)</option>
44 <option value="ncbi">NCBI style FASTA (m)</option>
45 <option value="nexus">Nexus/PAUP (m)</option>
46 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
47 <option value="phylip">PHYLIP interleaved (m)</option>
48 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
49 <option value="selex">SELEX (m)</option>
50 <option value="staden">Staden (s)</option>
51 <option value="strider">DNA strider (m)</option>
52 <option value="swiss">SwisProt entry (m)</option>
53 <option value="text">Plain sequence (s)</option>
54 <option value="treecon">Treecon (m)</option>
55 </param>
56 -->
57 </inputs>
58 <outputs>
59 <data format="coderet" name="out_file1" />
60 </outputs>
61 <tests>
62 <test>
63 <param name="input1" value="2.fasta"/>
64 <output name="out_file1" file="emboss_coderet_out.coderet"/>
65 </test>
66 </tests>
67 <code file="emboss_format_corrector.py" />
68 <help>
69 You can view the original documentation here_.
70
71 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/coderet.html
72
73 ------
74
75 **Citation**
76
77 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;`_
78
79 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;`_
80 </help>
81 </tool>