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comparison tools/protein_analysis/effectiveT3.xml @ 0:43436379876f

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Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:21:30 -0400
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-1:000000000000 0:43436379876f
1 <tool id="effectiveT3" name="Effective T3" version="0.0.7">
2 <description>Find bacterial effectors in protein sequences</description>
3 <command interpreter="python">
4 effectiveT3.py $module.fields.path
5 #if $restrict.type=="cutoff":
6 cutoff=$restrict.cutoff
7 #else:
8 $restrict.type
9 #end if
10 $fasta_file $tabular_file</command>
11 <inputs>
12 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
13 <param name="module" type="select" display="radio" label="Classification module">
14 <options from_file="effectiveT3.loc">
15 <column name="value" index="0"/>
16 <column name="name" index="1"/>
17 <column name="path" index="2"/>
18 </options>
19 </param>
20 <conditional name="restrict">
21 <param name="type" type="select" label="Cut-off setting">
22 <option value="selective">Selective (threshold set in module)</option>
23 <option value="sensitive">Sensitive (threshold set in module)</option>
24 <option value="cutoff">User defined cut-off</option>
25 </param>
26 <when value="selective" />
27 <when value="sensitive" />
28 <when value="cutoff" >
29 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" />
30 </when>
31 </conditional>
32 </inputs>
33 <outputs>
34 <data name="tabular_file" format="tabular" label="$module.value_label results" />
35 </outputs>
36 <help>
37
38 **What it does**
39
40 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.
41
42 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):
43
44 * Sequence identifier
45 * Sequence description (from the FASTA file)
46 * Score (between 0 and 1, or negative for an error such as a very short peptide)
47 * Predicted effector (true/false)
48
49 **References**
50
51 Jehl, Arnold and Rattei.
52 Effective - a database of predicted secreted bacterial proteins
53 Nucleic Acids Research, 39(Database issue), D591-5, 2011.
54 http://dx.doi.org/10.1093/nar/gkq1154
55
56 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
57 Sequence-based prediction of type III secreted proteins.
58 PLoS Pathog. 5(4):e1000376, 2009.
59 http://dx.doi.org/10.1371/journal.ppat.1000376
60
61 http://effectors.org/
62
63 </help>
64 </tool>