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comparison emboss_sigcleave.xml @ 10:9b98d3d903c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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9:18a63c800a4d 10:9b98d3d903c6
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" 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
55 ------
56
57 **Citation**
58
59 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
60
61 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
62 </help>
63 </tool>