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comparison emboss_oddcomp.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: oddcomp64" name="oddcomp" version="5.0.0"> 1 <tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0.1">
2 <!-- output contains file location info, commented out functional tests --> 2 <!-- output contains file location info, commented out functional tests -->
3 <description>Find protein sequence regions with a biased composition</description> 3 <description>Find protein sequence regions with a biased composition</description>
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 4 <macros>
5 <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command> 5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command>oddcomp -sequence '$input1' -infile '$input2' -outfile '$out_file1' -window $window -ignorebz $ignorebz -auto</command>
6 <inputs> 9 <inputs>
7 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Sequences" />
8 <label>Sequences</label> 11 <param name="input2" type="data" format="data" label="Dataset in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis" />
9 </param> 12 <param name="window" type="integer" value="30" label="Size of window in which to count" help="If you want to count frequencies in a 40 aa stretch you should enter 40 here" />
10 <param format="data" name="input2" type="data"> 13 <param name="ignorebz" type="select" label="Ignore B and Z" help="The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of 'Other' words">
11 <label>This is a file in the format of the output produced by 'compseq' that is used to set the minimum frequencies of words in this analysis</label>
12 </param>
13 <param name="window" type="text" value="30">
14 <label>This is the size of window in which to count. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here</label>
15 </param>
16 <param name="ignorebz" type="select">
17 <label>The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words
18 containing them, just noting them in the count of 'Other' words</label>
19 <option value="yes">Yes</option> 14 <option value="yes">Yes</option>
20 <option value="no">No</option> 15 <option value="no">No</option>
21 </param> 16 </param>
22 </inputs> 17 </inputs>
23 <outputs> 18 <outputs>
24 <data format="oddcomp" name="out_file1" /> 19 <data name="out_file1" format="oddcomp" />
25 </outputs> 20 </outputs>
26 <!-- <tests> 21 <!-- <tests>
27 <test> 22 <test>
28 <param name="input1" value="2.fasta"/> 23 <param name="input1" value="2.fasta"/>
29 <param name="input2" value="emboss_compseq_out.compseq"/> 24 <param name="input2" value="emboss_compseq_out.compseq"/>
32 <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/> 27 <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
33 </test> 28 </test>
34 </tests> --> 29 </tests> -->
35 <help> 30 <help>
36 You can view the original documentation here_. 31 You can view the original documentation here_.
37
38 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html
39 32
40 ------ 33 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/oddcomp.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> 34 </help>
35 <expand macro="citations" />
48 </tool> 36 </tool>