root/galaxy-central/tools/emboss_5/emboss_sigcleave.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: sigcleave88" name="sigcleave" version="5.0.0">
2  <description>Reports protein signal cleavage sites</description>
3  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4  <command>sigcleave -sequence $input1 -outfile $out_file1 -minweight "$minweight" -prokaryote $prokaryote -rformat2 $out_format1 -auto</command>
5  <inputs>
6    <param format="data" name="input1" type="data">
7      <label>Sequences</label>
8    </param>
9    <param name="minweight" size="4" type="text" value="3.5">
10      <label>Minimum scoring weight value for the predicted cleavage site</label>
11    </param>
12    <param name="prokaryote" type="select">
13      <label>Specifies the sequence is prokaryotic and changes the default scoring data file</label>
14      <option value="no">No</option>
15      <option value="yes">Yes</option>
16    </param>
17    <param name="out_format1" type="select">
18      <label>Output Report File Format</label>
19      <option value="motif">Motif</option>
20      <option value="embl">EMBL</option>
21      <option value="genbank">GENBANK</option>
22      <option value="gff">GFF</option>
23      <option value="pir">PIR</option>
24      <option value="swiss">SwissProt</option>
25      <option value="dbmotif">DbMotif</option>
26      <option value="diffseq">Diffseq</option>
27      <option value="excel">Excel (tab delimited)</option>
28      <option value="feattable">FeatTable</option>
29      <option value="regions">Regions</option>
30      <option value="seqtable">SeqTable</option>
31      <option value="simple">SRS Simple</option>
32      <option value="srs">SRS</option>
33      <option value="table">Table</option>
34      <option value="tagseq">TagSeq</option>
35    </param>
36  </inputs>
37  <outputs>
38    <data format="motif" name="out_file1" />
39  </outputs>
40  <tests>
41    <test>
42      <param name="input1" value="2.fasta"/>
43      <param name="minweight" value="3.5"/>
44      <param name="prokaryote" value="no"/>
45      <param name="out_format1" value="excel"/>
46      <output name="out_file1" file="emboss_sigcleave_out.tabular"/>
47    </test>
48  </tests>
49  <code file="emboss_format_corrector.py" />
50  <help>
51    You can view the original documentation here_.
52   
53    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sigcleave.html
54  </help>
55</tool>
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