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comparison emboss_coderet.xml @ 10:d49956b87f7e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:42:22 -0500
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children 8992d258e42f
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9:511429456d3c 10:d49956b87f7e
1 <tool id="EMBOSS: coderet13" name="coderet" version="5.0.0">
2 <description>Extract CDS, mRNA and translations from feature tables</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <!-- <command>coderet -seqall '$input1' -outfile '$out_file1' -osformat2 $out_format1 -cds $cds -mrna $mrna -translation $translation -auto</command>-->
9 <command>coderet -seqall '$input1' -outfile '$out_file1' -auto</command>
10 <inputs>
11 <param name="input1" type="data" format="data" label="On query" />
12 <!--
13 <param name="cds" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Extract CDS sequences" />
14 <param name="mrna" type="select" label="Extract mRNA sequences">
15 <option value="yes">Yes</option>
16 <option value="no">No</option>
17 </param>
18 <param name="translation" type="select" label="Extract translated sequences">
19 <option value="yes">Yes</option>
20 <option value="no">No</option>
21 </param>
22 <param name="out_format1" type="select" label="Output sequence file format">
23 <option value="fasta">FASTA (m)</option>
24 <option value="acedb">ACeDB (m)</option>
25 <option value="asn1">ASN.1 (m)</option>
26 <option value="clustal">Clustal (m)</option>
27 <option value="codata">CODATA (m)</option>
28 <option value="embl">EMBL (m)</option>
29 <option value="fitch">Fitch (m)</option>
30 <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
31 <option value="genbank">GENBANK (m)</option>
32 <option value="gff">GFF (m)</option>
33 <option value="hennig86">Hennig86 (m)</option>
34 <option value="ig">Intelligenetics (m)</option>
35 <option value="jackknifer">Jackknifer (m)</option>
36 <option value="jackknifernon">Jackknifernon (m)</option>
37 <option value="mega">Mega (m)</option>
38 <option value="meganon">Meganon (m)</option>
39 <option value="msf">Wisconsin Package GCG's MSF (m)</option>
40 <option value="pir">NBRF (PIR) (m)</option>
41 <option value="ncbi">NCBI style FASTA (m)</option>
42 <option value="nexus">Nexus/PAUP (m)</option>
43 <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
44 <option value="phylip">PHYLIP interleaved (m)</option>
45 <option value="phylipnon">PHYLIP non-interleaved (m)</option>
46 <option value="selex">SELEX (m)</option>
47 <option value="staden">Staden (s)</option>
48 <option value="strider">DNA strider (m)</option>
49 <option value="swiss">SwisProt entry (m)</option>
50 <option value="text">Plain sequence (s)</option>
51 <option value="treecon">Treecon (m)</option>
52 </param>
53 -->
54 </inputs>
55 <outputs>
56 <data name="out_file1" format="coderet" />
57 </outputs>
58 <tests>
59 <test>
60 <param name="input1" value="2.fasta"/>
61 <output name="out_file1" file="emboss_coderet_out.coderet"/>
62 </test>
63 </tests>
64 <help>
65 You can view the original documentation here_.
66
67 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/coderet.html
68 </help>
69 <expand macro="citations" />
70 </tool>