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

リビジョン 2, 2.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="EMBOSS: etandem33" name="etandem" version="5.0.0">
2  <description>Looks for tandem repeats in a nucleotide sequence</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>etandem -sequence $input1 -outfile $out_file1 -origfile $ofile2 -minrepeat $minrepeat -maxrepeat $maxrepeat -threshold $threshold -mismatch $mismatch -uniform $uniform -rformat2 $out_format1 -auto</command>
5  <inputs>
6    <param format="fasta" name="input1" type="data">
7      <label>Sequence</label>
8    </param>
9    <param name="minrepeat" size="4" type="text" value="10">
10      <label>Minimum repeat size</label>
11    </param>
12    <param name="maxrepeat" size="4" type="text" value="10">
13      <label>Maximum repeat size</label>
14    </param>
15    <param name="threshold" size="4" type="text" value="20">
16      <label>Threshold score</label>
17    </param>
18    <param name="mismatch" type="select">
19      <label>Allow N as a mismatch</label>
20      <option value="no">No</option>
21      <option value="yes">Yes</option>
22    </param>
23    <param name="uniform" type="select">
24      <label>Allow uniform consensus</label>
25      <option value="no">No</option>
26      <option value="yes">Yes</option>
27    </param>
28    <param name="out_format1" type="select">
29      <label>Output Report File Format</label>
30      <option value="table">Table</option>
31      <option value="embl">EMBL</option>
32      <option value="genbank">GENBANK</option>
33      <option value="gff">GFF</option>
34      <option value="pir">PIR</option>
35      <option value="swiss">SwissProt</option>
36      <option value="dbmotif">DbMotif</option>
37      <option value="diffseq">Diffseq</option>
38      <option value="excel">Excel (tab delimited)</option>
39      <option value="feattable">FeatTable</option>
40      <option value="motif">Motif</option>
41      <option value="regions">Regions</option>
42      <option value="seqtable">SeqTable</option>
43      <option value="simple">SRS Simple</option>
44      <option value="srs">SRS</option>
45      <option value="tagseq">TagSeq</option>
46    </param>
47  </inputs>
48  <outputs>
49    <data format="etandem" name="out_file1" />
50    <data format="table" name="ofile2" />   
51  </outputs>
52    <tests>
53    <test>
54      <param name="input1" value="1.fasta"/>
55      <param name="minrepeat" value="10"/>
56      <param name="maxrepeat" value="10"/>
57      <param name="threshold" value="20"/>
58      <param name="mismatch" value="no"/>
59       <param name="uniform" value="no"/>
60      <param name="out_format1" value="table"/>
61      <output name="ofile2" file="emboss_etandem_out.table"/>
62    </test>
63  </tests>
64  <code file="emboss_format_corrector.py" />
65  <help>
66.. class:: warningmark
67
68The input dataset needs to be sequences.
69
70-----
71
72    You can view the original documentation here_.
73   
74    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/etandem.html
75  </help>
76</tool>
77
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