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comparison emboss_cpgplot.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: cpgplot15" name="cpgplot" version="5.0.0"> 1 <tool id="EMBOSS: cpgplot15" name="cpgplot" version="5.0.0">
2 <description>Plot CpG rich areas</description> 2 <description>Plot CpG rich areas</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command interpreter="perl">emboss_cpgplot_wrapper.pl cpgplot -sequence $input1 -window $window -minlen $minlen -minpc $minpc -outfile $outfile -graph png -goutfile $goutfile -outfeat $outfeat -minoe $minoe -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>perl '$__tool_directory__/emboss_cpgplot_wrapper.pl' cpgplot -sequence '$input1' -window $window -minlen $minlen -minpc $minpc -outfile '$outfile' -graph png -goutfile '$goutfile' -outfeat '$outfeat' -minoe $minoe -auto</command>
5 <inputs> 9 <inputs>
6 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="On query" />
7 <label>On query</label> 11 <param name="window" type="integer" value="100" label="Window size" />
8 </param> 12 <param name="minlen" type="integer" value="200" label="Minimum length" />
9 <param name="window" type="integer" value="100"> 13 <param name="minoe" type="float" value="0.6" label="Minimum average observed to expected ratio" />
10 <label>Window Size</label> 14 <param name="minpc" type="float" value="50.0" label="Minimum average percentage of G plus C" />
11 </param>
12 <param name="minlen" type="integer" value="200">
13 <label>Minimum length</label>
14 </param>
15 <param name="minoe" type="float" value="0.6">
16 <label>Minimum average observed to expected ratio</label>
17 </param>
18 <param name="minpc" type="float" value="50.0">
19 <label>Minimum average percentage of G plus C</label>
20 </param>
21 </inputs> 15 </inputs>
22 <outputs> 16 <outputs>
23 <data format="cpgplot" name="outfile" /> 17 <data name="outfile" format="cpgplot" />
24 <data format="png" name="goutfile" /> 18 <data name="goutfile" format="png" />
25 <data format="gff" name="outfeat" /> 19 <data name="outfeat" format="gff" />
26 </outputs> 20 </outputs>
27 <code file="emboss_format_corrector.py" />
28 <help> 21 <help>
29 You can view the original documentation here_. 22 You can view the original documentation here_.
30
31 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/cpgplot.html
32 23
33 ------ 24 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/cpgplot.html
34
35 **Citation**
36
37 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;`_
38
39 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;`_
40 </help> 25 </help>
26 <expand macro="citations" />
41 </tool> 27 </tool>