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comparison emboss_wordcount.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: wordcount109" name="wordcount" version="5.0.0"> 1 <tool id="EMBOSS: wordcount109" name="wordcount" version="5.0.0.1">
2 <description>Counts words of a specified size in a DNA sequence</description> 2 <description>Counts words of a specified size in a DNA sequence</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>wordcount -sequence $input1 -outfile $out_file1 -wordsize "$wordsize" -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>wordcount -sequence '$input1' -outfile '$out_file1' -wordsize $wordsize -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="wordsize" type="integer" value="4" label="Word size" />
8 </param>
9 <param name="wordsize" type="text" value="4">
10 <label>Word size</label>
11 </param>
12 </inputs> 11 </inputs>
13 <outputs> 12 <outputs>
14 <data format="wordcount" name="out_file1" /> 13 <data name="out_file1" format="wordcount" />
15 </outputs> 14 </outputs>
16 <tests> 15 <tests>
17 <test> 16 <test>
18 <param name="input1" value="2.fasta"/> 17 <param name="input1" value="2.fasta"/>
19 <param name="wordsize" value="4"/> 18 <param name="wordsize" value="4"/>
20 <output name="out_file1" file="emboss_wordcount_out.wordcount"/> 19 <output name="out_file1" file="emboss_wordcount_out.wordcount"/>
21 </test> 20 </test>
22 </tests> 21 </tests>
23 <help> 22 <help>
23 .. class:: warningmark
24 24
25 .. class:: warningmark 25 The input dataset needs to be sequences.
26 26
27 The input dataset needs to be sequences. 27 -----
28
29 -----
30 28
31 You can view the original documentation here_. 29 You can view the original documentation here_.
32
33 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordcount.html
34 30
35 ------ 31 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/wordcount.html
36
37 **Citation**
38
39 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;`_
40
41 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;`_
42 </help> 32 </help>
33 <expand macro="citations" />
43 </tool> 34 </tool>