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