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annotate emboss_garnier.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: garnier40" name="garnier" version="5.0.0">
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2 <description>Predicts protein secondary structure</description>
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3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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4 <command>garnier -sequence $input1 -outfile $out_file1 -idc $idc -rformat2 $out_format1 -auto</command>
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5 <inputs>
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6 <param format="data" name="input1" type="data">
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7 <label>Sequences</label>
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8 </param>
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9 <param name="idc" type="select">
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10 <label>In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. 'idc' is an index into a
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11 set of arrays, dharr[] and dsarr[], which provide 'decision constants' (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don't
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12 use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used</label>
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13 <option value="0">idc 0</option>
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14 <option value="1">idc 1</option>
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15 <option value="2">idc 2</option>
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16 <option value="3">idc 3</option>
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17 <option value="4">idc 4</option>
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18 <option value="5">idc 5</option>
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19 <option value="6">idc 6</option>
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20 </param>
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21 <param name="out_format1" type="select">
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22 <label>Output Report File Format</label>
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23 <option value="tagseq">TagSeq</option>
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24 <option value="embl">EMBL</option>
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25 <option value="genbank">GENBANK</option>
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26 <option value="gff">GFF</option>
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27 <option value="pir">PIR</option>
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28 <option value="swiss">SwissProt</option>
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29 <option value="dbmotif">DbMotif</option>
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30 <option value="diffseq">Diffseq</option>
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31 <option value="excel">Excel (tab delimited)</option>
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32 <option value="feattable">FeatTable</option>
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33 <option value="motif">Motif</option>
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34 <option value="regions">Regions</option>
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35 <option value="seqtable">SeqTable</option>
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36 <option value="simple">SRS Simple</option>
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37 <option value="srs">SRS</option>
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38 <option value="table">Table</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data format="garnier" name="out_file1" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input1" value="2.fasta"/>
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47 <param name="idc" value="0"/>
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48 <param name="out_format1" value="excel"/>
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49 <output name="out_file1" file="emboss_garnier_out.tabular"/>
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50 </test>
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51 </tests>
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52 <code file="emboss_format_corrector.py" />
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53 <help>
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54 You can view the original documentation here_.
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55
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56 .. _here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/garnier.html
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57
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58 ------
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59
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60 **Citation**
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61
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62 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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63
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64 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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65 </help>
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66 </tool>