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annotate emboss_oddcomp.xml @ 10:9b98d3d903c6 draft

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author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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1 <tool id="EMBOSS: oddcomp64" name="oddcomp" version="5.0.0">
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2 <!-- output contains file location info, commented out functional tests -->
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3 <description>Find protein sequence regions with a biased composition</description>
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4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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5 <command>oddcomp -sequence $input1 -infile $input2 -outfile $out_file1 -window $window -ignorebz $ignorebz -auto</command>
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6 <inputs>
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7 <param format="data" name="input1" type="data">
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8 <label>Sequences</label>
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9 </param>
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10 <param format="data" name="input2" type="data">
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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>
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12 </param>
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13 <param name="window" type="text" value="30">
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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>
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15 </param>
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16 <param name="ignorebz" type="select">
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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
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18 containing them, just noting them in the count of 'Other' words</label>
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19 <option value="yes">Yes</option>
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20 <option value="no">No</option>
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data format="oddcomp" name="out_file1" />
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25 </outputs>
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26 <!-- <tests>
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27 <test>
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28 <param name="input1" value="2.fasta"/>
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29 <param name="input2" value="emboss_compseq_out.compseq"/>
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30 <param name="window" value="30"/>
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31 <param name="ignorebz" value="yes"/>
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32 <output name="out_file1" file="emboss_oddcomp_out.oddcomp"/>
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33 </test>
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34 </tests> -->
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35 <help>
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36 You can view the original documentation here_.
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37
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38 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/oddcomp.html
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39
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40 ------
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41
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42 **Citation**
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43
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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;`_
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45
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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;`_
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47 </help>
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48 </tool>