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annotate tools/protein_analysis/effectiveT3.xml @ 1:e607c342312f

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Wrapper v0.0.8, includes effectiveT3.loc.sample file
author peterjc
date Tue, 02 Aug 2011 07:06:13 -0400
parents 43436379876f
children 5a8e09f115f8
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e607c342312f Wrapper v0.0.8, includes effectiveT3.loc.sample file
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1 <tool id="effectiveT3" name="Effective T3" version="0.0.8">
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2 <description>Find bacterial effectors in protein sequences</description>
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3 <command interpreter="python">
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4 effectiveT3.py $module.fields.path
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5 #if $restrict.type=="cutoff":
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6 cutoff=$restrict.cutoff
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7 #else:
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8 $restrict.type
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9 #end if
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10 $fasta_file $tabular_file</command>
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11 <inputs>
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12 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
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13 <param name="module" type="select" display="radio" label="Classification module">
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14 <options from_file="effectiveT3.loc">
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15 <column name="value" index="0"/>
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16 <column name="name" index="1"/>
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17 <column name="path" index="2"/>
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18 </options>
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19 </param>
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20 <conditional name="restrict">
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21 <param name="type" type="select" label="Cut-off setting">
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22 <option value="selective">Selective (threshold set in module)</option>
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23 <option value="sensitive">Sensitive (threshold set in module)</option>
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24 <option value="cutoff">User defined cut-off</option>
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25 </param>
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26 <when value="selective" />
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27 <when value="sensitive" />
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28 <when value="cutoff" >
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29 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" />
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30 </when>
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31 </conditional>
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32 </inputs>
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33 <outputs>
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34 <data name="tabular_file" format="tabular" label="$module.value_label results" />
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35 </outputs>
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36 <help>
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37
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38 **What it does**
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39
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40 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.
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41
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42 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):
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43
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44 * Sequence identifier
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45 * Sequence description (from the FASTA file)
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46 * Score (between 0 and 1, or negative for an error such as a very short peptide)
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47 * Predicted effector (true/false)
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48
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49 **References**
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50
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51 Jehl, Arnold and Rattei.
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52 Effective - a database of predicted secreted bacterial proteins
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53 Nucleic Acids Research, 39(Database issue), D591-5, 2011.
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54 http://dx.doi.org/10.1093/nar/gkq1154
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55
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56 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
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57 Sequence-based prediction of type III secreted proteins.
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58 PLoS Pathog. 5(4):e1000376, 2009.
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59 http://dx.doi.org/10.1371/journal.ppat.1000376
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60
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61 http://effectors.org/
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62
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63 </help>
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64 </tool>