root/galaxy-central/tools/emboss_5/emboss_equicktandem.xml

リビジョン 2, 2.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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
52The 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>
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