Mercurial > repos > devteam > emboss_5
annotate emboss_5/emboss_newcpgreport.xml @ 8:b810c96613ee draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:12:41 -0500 |
parents | b94ca591877b |
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rev | line source |
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0 | 1 <tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0"> |
2 <description>Report CpG rich areas</description> | |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
4 <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command> | |
5 <inputs> | |
6 <param format="data" name="input1" type="data"> | |
7 <label>Sequence</label> | |
8 </param> | |
8
b810c96613ee
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit a1517c9d22029095120643bbe2c8fa53754dd2b7
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9 <param name="window" type="text" value="100"> |
0 | 10 <label>Window Size</label> |
11 </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
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12 <param name="shift" type="text" value="1"> |
0 | 13 <label>Step size (shift)</label> |
14 </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
|
15 <param name="minlen" type="text" value="200"> |
0 | 16 <label>Minimum length</label> |
17 </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
|
18 <param name="minoe" type="text" value="0.6"> |
0 | 19 <label>Minimum average observed to expected ratio</label> |
20 </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
|
21 <param name="minpc" type="text" value="50.0"> |
0 | 22 <label>Minimum average percentage of G plus C</label> |
23 </param> | |
24 </inputs> | |
25 <outputs> | |
26 <data format="newcpgreport" name="out_file1" /> | |
27 </outputs> | |
28 <tests> | |
29 <test> | |
30 <param name="input1" value="2.fasta"/> | |
31 <param name="window" value="100"/> | |
32 <param name="shift" value="1"/> | |
33 <param name="minlen" value="200"/> | |
34 <param name="minoe" value="0.6"/> | |
35 <param name="minpc" value="50.0"/> | |
36 <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/> | |
37 </test> | |
38 </tests> | |
39 <help> | |
40 You can view the original documentation here_. | |
41 | |
42 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html | |
43 | |
44 ------ | |
45 | |
46 **Citation** | |
47 | |
48 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>`_ | |
49 | |
50 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>`_ | |
51 </help> | |
52 </tool> |