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comparison emboss_fuzzpro.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: fuzzpro38" name="fuzzpro" version="5.0.0.1">
2 <description>Protein 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>fuzzpro -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -rformat2 $out_format1 -auto</command>
9 <inputs>
10 <param name="input1" type="data" format="data" label="Sequences" />
11 <param name="pattern" type="text" value="" label="Search pattern">
12 <sanitizer>
13 <valid initial="string.printable">
14 <remove value="&apos;"/>
15 </valid>
16 <mapping initial="none">
17 <add source="&apos;" target=""/>
18 </mapping>
19 </sanitizer>
20 </param>
21 <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
22 <param name="out_format1" type="select" label="Output report file format">
23 <option value="seqtable">SeqTable</option>
24 <option value="embl">EMBL</option>
25 <option value="genbank">GENBANK</option>
26 <option value="gff">GFF</option>
27 <option value="pir">PIR</option>
28 <option value="swiss">SwissProt</option>
29 <option value="dbmotif">DbMotif</option>
30 <option value="diffseq">Diffseq</option>
31 <option value="excel">Excel (tab delimited)</option>
32 <option value="feattable">FeatTable</option>
33 <option value="motif">Motif</option>
34 <option value="regions">Regions</option>
35 <option value="simple">SRS Simple</option>
36 <option value="srs">SRS</option>
37 <option value="table">Table</option>
38 <option value="tagseq">TagSeq</option>
39 </param>
40 </inputs>
41 <outputs>
42 <data name="out_file1" format="fuzzpro" />
43 </outputs>
44 <help>
45 You can view the original documentation here_.
46
47 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzzpro.html
48 </help>
49 <expand macro="citations" />
50 </tool>