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comparison emboss_chips.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: chips10" name="chips" version="5.0.0"> 1 <tool id="EMBOSS: chips10" name="chips" version="5.0.0">
2 <description>Codon usage statistics</description> 2 <description>Codon usage statistics</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>chips -seqall $input1 -outfile $out_file1 -sum $sum -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command>chips -seqall '$input1' -outfile '$out_file1' -sum $sum -auto</command>
5 <inputs> 8 <inputs>
6 <param format="data" name="input1" type="data"> 9 <param name="input1" type="data" format="data" label="On query" />
7 <label>On query</label> 10 <param name="sum" type="select" label="Sum codons over all sequences">
8 </param>
9 <param name="sum" type="select">
10 <label>Sum codons over all sequences</label>
11 <option value="yes">Yes</option> 11 <option value="yes">Yes</option>
12 <option value="no">No</option> 12 <option value="no">No</option>
13 </param> 13 </param>
14 </inputs> 14 </inputs>
15 <outputs> 15 <outputs>
16 <data format="chips" name="out_file1" /> 16 <data name="out_file1" format="chips" />
17 </outputs> 17 </outputs>
18 <tests> 18 <tests>
19 <test> 19 <test>
20 <param name="input1" value="2.fasta"/> 20 <param name="input1" value="2.fasta"/>
21 <param name="sum" value="yes"/> 21 <param name="sum" value="yes"/>
22 <output name="out_file1" file="emboss_chips_out.chips"/> 22 <output name="out_file1" file="emboss_chips_out.chips"/>
23 </test> 23 </test>
24 </tests> 24 </tests>
25 <help> 25 <help>
26 You can view the original documentation here_. 26 You can view the original documentation here_.
27
28 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/chips.html
29 27
30 ------ 28 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/chips.html
31
32 **Citation**
33
34 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;`_
35
36 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;`_
37 </help> 29 </help>
30 <expand macro="citations" />
38 </tool> 31 </tool>