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comparison emboss_newcpgreport.xml @ 11:0e2484b6829b draft

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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
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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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
51 </help> 34 </help>
35 <expand macro="citations" />
52 </tool> 36 </tool>