comparison emboss_cpgreport.xml @ 10:9b98d3d903c6 draft

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: cpgreport16" name="cpgreport" version="5.0.0">
2 <description>Reports all CpG rich regions</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
4 <command><![CDATA[
5 cpgreport
6 -sequence '$input1'
7 -outfile '$out_file1'
8 -outfeat '$out_file2'
9 -offormat3 '$out_format2'
10 -score '$score'
11 -auto
12 ]]>
13 </command>
14 <inputs>
15 <param format="fasta" name="input1" type="data">
16 <label>On query</label>
17 </param>
18 <param name="score" type="text" value="17">
19 <label>Score for each CG sequence found (1-200)</label>
20 </param>
21 <param name="out_format2" type="select" label="Output Feature File Format">
22 <option value="gff">GFF</option>
23 <option value="embl">EMBL</option>
24 <option value="swiss">SwissProt</option>
25 </param>
26 </inputs>
27 <outputs>
28 <data format="cpgreport" name="out_file1" />
29 <data format="gff" name="out_file2" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="input1" value="2.fasta"/>
34 <param name="score" value="17"/>
35 <param name="out_format2" value="embl"/>
36 <output name="out_file1" file="emboss_cpgreport_out2.cpgreport"/>
37 </test>
38 <!-- <test>
39 <param name="input1" value="2.fasta"/>
40 <param name="score" value="17"/>
41 <param name="out_format2" value="gff"/>
42 <output name="out_file1" file="emboss_cpgreport_out1.gff"/>
43 </test> -->
44 </tests>
45 <code file="emboss_format_corrector.py" />
46 <help>
47 .. class:: warningmark
48
49 The input dataset needs to be sequences.
50
51 -----
52
53 You can view the original documentation here_.
54
55 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html
56
57 ------
58
59 **Citation**
60
61 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;`_
62
63 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;`_
64 </help>
65 </tool>