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comparison emboss_plotcon.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: plotcon75" name="plotcon" version="5.0.0"> 1 <tool id="EMBOSS: plotcon75" name="plotcon" version="5.0.0.1">
2 <!-- produces png file --> 2 <!-- produces png file -->
3 <description>Plot quality of conservation of a sequence alignment</description> 3 <description>Plot quality of conservation of a sequence alignment</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl plotcon -sequences $input1 -graph png -goutfile $out_file1 -winsize $winsize -auto</command> 5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' plotcon -sequences '$input1' -graph png -goutfile '$out_file1' -winsize $winsize -auto</command>
6 <inputs> 9 <inputs>
7 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Sequence" />
8 <label>Sequence</label> 11 <param name="winsize" type="integer" value="4" label="Number of columns to average alignment quality over" />
9 </param>
10 <param name="winsize" type="text" value="4">
11 <label>Number of columns to average alignment quality over</label>
12 </param>
13 </inputs> 12 </inputs>
14 <outputs> 13 <outputs>
15 <data format="png" name="out_file1" /> 14 <data name="out_file1" format="png" />
16 </outputs> 15 </outputs>
17 <help> 16 <help>
18 You can view the original documentation here_. 17 You can view the original documentation here_.
19
20 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/plotcon.html
21 18
22 ------ 19 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/plotcon.html
23
24 **Citation**
25
26 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;`_
27
28 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;`_
29 </help> 20 </help>
21 <expand macro="citations" />
30 </tool> 22 </tool>