Mercurial > repos > devteam > emboss_5
comparison emboss_fuzznuc.xml @ 10:d49956b87f7e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author | iuc |
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date | Wed, 08 Feb 2017 12:42:22 -0500 |
parents | |
children | 63dd26468588 |
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9:511429456d3c | 10:d49956b87f7e |
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1 <tool id="EMBOSS: fuzznuc37" name="fuzznuc" version="5.0.2"> | |
2 <description>Nucleic acid pattern search</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <code file="emboss_format_corrector.py" /> | |
8 <command>fuzznuc -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -complement $complement -rformat2 $out_format1 -auto</command> | |
9 <inputs> | |
10 <param name="input1" type="data" format="fasta" label="Sequences" /> | |
11 <param name="pattern" type="text" value="" label="Search pattern"> | |
12 <sanitizer> | |
13 <valid initial="string.printable"> | |
14 <remove value="'"/> | |
15 </valid> | |
16 <mapping initial="none"> | |
17 <add source="'" target=""/> | |
18 </mapping> | |
19 </sanitizer> | |
20 </param> | |
21 <param name="mismatch" type="integer" value="0" label="Number of mismatches" /> | |
22 <param name="complement" type="select" label="Search complementary strand"> | |
23 <option value="no">No</option> | |
24 <option value="yes">Yes</option> | |
25 </param> | |
26 <param name="out_format1" type="select" label="Output report file format"> | |
27 <option value="seqtable">SeqTable</option> | |
28 <option value="embl">EMBL</option> | |
29 <option value="genbank">GENBANK</option> | |
30 <option value="gff">GFF</option> | |
31 <option value="pir">PIR</option> | |
32 <option value="swiss">SwissProt</option> | |
33 <option value="dbmotif">DbMotif</option> | |
34 <option value="diffseq">Diffseq</option> | |
35 <option value="excel">Excel (tab delimited)</option> | |
36 <option value="feattable">FeatTable</option> | |
37 <option value="motif">Motif</option> | |
38 <option value="regions">Regions</option> | |
39 <option value="simple">SRS Simple</option> | |
40 <option value="fuzznuc">Fuzznuc Output File</option> | |
41 <option value="srs">SRS</option> | |
42 <option value="table">Table</option> | |
43 <option value="tagseq">TagSeq</option> | |
44 </param> | |
45 </inputs> | |
46 <outputs> | |
47 <data name="out_file1" format="fuzznuc" /> | |
48 </outputs> | |
49 <tests> | |
50 <test> | |
51 <param name="input1" value="2.fasta"/> | |
52 <param name="pattern" value="AA"/> | |
53 <param name="mismatch" value="0"/> | |
54 <param name="complement" value="no"/> | |
55 <param name="out_format1" value="excel"/> | |
56 <output name="out_file1" file="emboss_fuzznuc_out.tabular"/> | |
57 </test> | |
58 </tests> | |
59 <help> | |
60 .. class:: warningmark | |
61 | |
62 The input dataset needs to be sequences. | |
63 | |
64 ----- | |
65 | |
66 You can view the original documentation here_. | |
67 | |
68 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzznuc.html | |
69 </help> | |
70 <expand macro="citations" /> | |
71 </tool> |