comparison emboss_equicktandem.xml @ 10:d49956b87f7e draft

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: equicktandem31" name="equicktandem" version="5.0.0.1">
2 <description>Finds tandem repeats</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>equicktandem -sequence '$input1' -outfile '$out_file1' -origfile '$ofile2' -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command>
9 <inputs>
10 <param name="input1" type="data" format="fasta" label="Sequence" />
11 <param name="maxrepeat" type="integer" value="600" label="Maximum repeat size" />
12 <param name="threshold" type="integer" value="20" label="Threshold score" />
13 <param name="out_format1" type="select" label="Output report file format">
14 <option value="table">Table</option>
15 <option value="embl">EMBL</option>
16 <option value="genbank">GENBANK</option>
17 <option value="gff">GFF</option>
18 <option value="pir">PIR</option>
19 <option value="swiss">SwissProt</option>
20 <option value="dbmotif">DbMotif</option>
21 <option value="diffseq">Diffseq</option>
22 <option value="excel">Excel (tab delimited)</option>
23 <option value="feattable">FeatTable</option>
24 <option value="motif">Motif</option>
25 <option value="regions">Regions</option>
26 <option value="seqtable">SeqTable</option>
27 <option value="simple">SRS Simple</option>
28 <option value="srs">SRS</option>
29 <option value="tagseq">TagSeq</option>
30 </param>
31 </inputs>
32 <outputs>
33 <data name="out_file1" format="table" />
34 <data name="ofile2" format="equicktandem" />
35 </outputs>
36 <tests>
37 <test>
38 <param name="input1" value="1.fasta"/>
39 <param name="maxrepeat" value="600"/>
40 <param name="threshold" value="20"/>
41 <param name="out_format1" value="table"/>
42 <output name="ofile2" file="emboss_equicktandem_out.equicktandem"/>
43 </test>
44 </tests>
45 <help>
46 .. class:: warningmark
47
48 The input dataset needs to be sequences.
49
50 -----
51
52 You can view the original documentation here_.
53
54 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/equicktandem.html
55 </help>
56 <expand macro="citations" />
57 </tool>