Mercurial > repos > devteam > emboss_5
comparison emboss_newcpgreport.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author | iuc |
---|---|
date | Mon, 30 Jan 2017 13:27:40 -0500 |
parents | 9b98d3d903c6 |
children | 27c43fb015f0 |
comparison
equal
deleted
inserted
replaced
10:9b98d3d903c6 | 11:0e2484b6829b |
---|---|
1 <tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0"> | 1 <tool id="EMBOSS: newcpgreport57" name="newcpgreport" version="5.0.0.1"> |
2 <description>Report CpG rich areas</description> | 2 <description>Report CpG rich areas</description> |
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | 3 <macros> |
4 <command>newcpgreport -sequence $input1 -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile $out_file1 -minoe $minoe -auto</command> | 4 <import>macros.xml</import> |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command>newcpgreport -sequence '$input1' -window $window -shift $shift -minlen $minlen -minpc $minpc -outfile '$out_file1' -minoe $minoe -auto</command> | |
5 <inputs> | 8 <inputs> |
6 <param format="data" name="input1" type="data"> | 9 <param name="input1" type="data" format="data" label="Sequence" /> |
7 <label>Sequence</label> | 10 <param name="window" type="integer" value="100" label="Window size" /> |
8 </param> | 11 <param name="shift" type="integer" value="1" label="Step size (shift)" /> |
9 <param name="window" type="text" value="100"> | 12 <param name="minlen" type="integer" value="200" label="Minimum length" /> |
10 <label>Window Size</label> | 13 <param name="minoe" type="float" value="0.6" label="Minimum average observed to expected ratio" /> |
11 </param> | 14 <param name="minpc" type="float" value="50.0" label="Minimum average percentage of G plus C" /> |
12 <param name="shift" type="text" value="1"> | |
13 <label>Step size (shift)</label> | |
14 </param> | |
15 <param name="minlen" type="text" value="200"> | |
16 <label>Minimum length</label> | |
17 </param> | |
18 <param name="minoe" type="text" value="0.6"> | |
19 <label>Minimum average observed to expected ratio</label> | |
20 </param> | |
21 <param name="minpc" type="text" value="50.0"> | |
22 <label>Minimum average percentage of G plus C</label> | |
23 </param> | |
24 </inputs> | 15 </inputs> |
25 <outputs> | 16 <outputs> |
26 <data format="newcpgreport" name="out_file1" /> | 17 <data name="out_file1" format="newcpgreport" /> |
27 </outputs> | 18 </outputs> |
28 <tests> | 19 <tests> |
29 <test> | 20 <test> |
30 <param name="input1" value="2.fasta"/> | 21 <param name="input1" value="2.fasta"/> |
31 <param name="window" value="100"/> | 22 <param name="window" value="100"/> |
36 <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/> | 27 <output name="out_file1" file="emboss_newcpgreport_out.newcpgreport"/> |
37 </test> | 28 </test> |
38 </tests> | 29 </tests> |
39 <help> | 30 <help> |
40 You can view the original documentation here_. | 31 You can view the original documentation here_. |
41 | |
42 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/newcpgreport.html | |
43 | 32 |
44 ------ | 33 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/newcpgreport.html |
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> | 34 </help> |
35 <expand macro="citations" /> | |
52 </tool> | 36 </tool> |