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comparison emboss_wobble.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: wobble108" name="wobble" version="5.0.0"> 1 <tool id="EMBOSS: wobble108" name="wobble" version="5.0.0.1">
2 <description>Wobble base plot</description> 2 <description>Wobble base plot</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command interpreter="perl">emboss_single_outputfile_wrapper.pl wobble -sequence $input1 -graph png -goutfile $ofile1 -outfile $ofile2 -window "$window" -bases "$bases" -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' wobble -sequence '$input1' -graph png -goutfile '$ofile1' -outfile '$ofile2' -window $window -bases '$bases' -auto</command>
5 <inputs> 8 <inputs>
6 <param format="fasta" name="input1" type="data"> 9 <param name="input1" type="data" format="fasta" label="Sequence" />
7 <label>Sequence</label> 10 <param name="window" type="integer" value="30" label="Window size, in codons" />
8 </param> 11 <param name="bases" type="text" value="GC" label="Bases used" />
9 <param name="window" type="text" value="30">
10 <label>Window size, in codons</label>
11 </param>
12 <param name="bases" type="text" value="GC">
13 <label>Bases used</label>
14 </param>
15 </inputs> 12 </inputs>
16 <outputs> 13 <outputs>
17 <data format="png" name="ofile1" /> 14 <data name="ofile1" format="png" />
18 <data format="wobble" name="ofile2" /> 15 <data name="ofile2" format="wobble" />
19 </outputs> 16 </outputs>
20 <tests> 17 <tests>
21 <test> 18 <test>
22 <param name="input1" value="2.fasta"/> 19 <param name="input1" value="2.fasta"/>
23 <param name="window" value="30"/> 20 <param name="window" value="30"/>
24 <param name="bases" value="GC"/> 21 <param name="bases" value="GC"/>
25 <output name="ofile2" file="emboss_wobble_out.wobble"/> 22 <output name="ofile2" file="emboss_wobble_out.wobble"/>
26 </test> 23 </test>
27 </tests> 24 </tests>
28 <help> 25 <help>
26 .. class:: warningmark
29 27
30 .. class:: warningmark 28 The input dataset needs to be sequences.
31 29
32 The input dataset needs to be sequences. 30 -----
33
34 -----
35 31
36 You can view the original documentation here_. 32 You can view the original documentation here_.
37
38 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wobble.html
39 33
40 ------ 34 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wobble.html
41
42 **Citation**
43
44 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;`_
45
46 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;`_
47 </help> 35 </help>
36 <expand macro="citations" />
48 </tool> 37 </tool>