Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_equicktandem.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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1 <tool id="EMBOSS: equicktandem31" name="equicktandem" version="5.0.0"> | |
2 <description>Finds tandem repeats</description> | |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
4 <command>equicktandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -maxrepeat $maxrepeat -threshold $threshold -rformat2 $out_format1 -auto</command> | |
5 <inputs> | |
6 <param format="fasta" name="input1" type="data"> | |
7 <label>Sequence</label> | |
8 </param> | |
9 <param name="maxrepeat" size="4" type="text" value="600"> | |
10 <label>Maximum repeat size</label> | |
11 </param> | |
12 <param name="threshold" size="4" type="text" value="20"> | |
13 <label>Threshold score</label> | |
14 </param> | |
15 <param name="out_format1" type="select"> | |
16 <label>Output Report File Format</label> | |
17 <option value="table">Table</option> | |
18 <option value="embl">EMBL</option> | |
19 <option value="genbank">GENBANK</option> | |
20 <option value="gff">GFF</option> | |
21 <option value="pir">PIR</option> | |
22 <option value="swiss">SwissProt</option> | |
23 <option value="dbmotif">DbMotif</option> | |
24 <option value="diffseq">Diffseq</option> | |
25 <option value="excel">Excel (tab delimited)</option> | |
26 <option value="feattable">FeatTable</option> | |
27 <option value="motif">Motif</option> | |
28 <option value="regions">Regions</option> | |
29 <option value="seqtable">SeqTable</option> | |
30 <option value="simple">SRS Simple</option> | |
31 <option value="srs">SRS</option> | |
32 <option value="tagseq">TagSeq</option> | |
33 </param> | |
34 </inputs> | |
35 <outputs> | |
36 <data format="table" name="out_file1" /> | |
37 <data format="equicktandem" name="ofile2" /> | |
38 </outputs> | |
39 <tests> | |
40 <test> | |
41 <param name="input1" value="1.fasta"/> | |
42 <param name="maxrepeat" value="600"/> | |
43 <param name="threshold" value="20"/> | |
44 <param name="out_format1" value="table"/> | |
45 <output name="ofile2" file="emboss_equicktandem_out.equicktandem"/> | |
46 </test> | |
47 </tests> | |
48 <code file="emboss_format_corrector.py" /> | |
49 <help> | |
50 .. class:: warningmark | |
51 | |
52 The input dataset needs to be sequences. | |
53 | |
54 ----- | |
55 | |
56 You can view the original documentation here_. | |
57 | |
58 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/equicktandem.html | |
59 </help> | |
60 </tool> |