Mercurial > repos > devteam > emboss_5
annotate emboss_5/emboss_cpgreport.xml @ 8:b810c96613ee draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
---|---|
date | Wed, 11 Nov 2015 12:12:41 -0500 |
parents | b94ca591877b |
children |
rev | line source |
---|---|
0 | 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>cpgreport -sequence $input1 -outfile $out_file1 -outfeat $out_file2 -offormat3 $out_format2 -score $score -auto</command> | |
5 <inputs> | |
6 <param format="fasta" name="input1" type="data"> | |
7 <label>On query</label> | |
8 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents:
0
diff
changeset
|
9 <param name="score" type="text" value="17"> |
0 | 10 <label>Score for each CG sequence found (1-200)</label> |
11 </param> | |
12 <param name="out_format2" type="select"> | |
13 <label>Output Feature File Format</label> | |
14 <option value="gff">GFF</option> | |
15 <option value="embl">EMBL</option> | |
16 <option value="swiss">SwissProt</option> | |
17 </param> | |
18 </inputs> | |
19 <outputs> | |
20 <data format="cpgreport" name="out_file1" /> | |
21 <data format="gff" name="out_file2" /> | |
22 </outputs> | |
23 <tests> | |
24 <test> | |
25 <param name="input1" value="2.fasta"/> | |
26 <param name="score" value="17"/> | |
27 <param name="out_format2" value="gff"/> | |
28 <output name="out_file2" file="emboss_cpgreport_out2.cpgreport"/> | |
29 </test> | |
30 <!-- <test> | |
31 <param name="input1" value="2.fasta"/> | |
32 <param name="score" value="17"/> | |
33 <param name="out_format2" value="gff"/> | |
34 <output name="out_file1" file="emboss_cpgreport_out1.gff"/> | |
35 </test> --> | |
36 </tests> | |
37 <code file="emboss_format_corrector.py" /> | |
38 <help> | |
39 .. class:: warningmark | |
40 | |
41 The input dataset needs to be sequences. | |
42 | |
43 ----- | |
44 | |
45 You can view the original documentation here_. | |
46 | |
47 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgreport.html | |
48 | |
49 ------ | |
50 | |
51 **Citation** | |
52 | |
53 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. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
54 | |
55 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. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ | |
56 </help> | |
57 </tool> |