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comparison tools/effectiveT3/effectiveT3.xml @ 2:66e9d4c44ca2 draft

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Uploaded v0.0.11, auto installation
author peterjc
date Tue, 30 Apr 2013 09:32:56 -0400
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1:7479dbb285b5 2:66e9d4c44ca2
1 <tool id="effectiveT3" name="Effective T3" version="0.0.11">
2 <description>Find bacterial effectors in protein sequences</description>
3 <version_command interpreter="python">effectiveT3.py --version</version_command>
4 <command interpreter="python">
5 effectiveT3.py $module.fields.path
6 #if $restrict.type=="cutoff":
7 cutoff=$restrict.cutoff
8 #else:
9 $restrict.type
10 #end if
11 $fasta_file $tabular_file</command>
12 <stdio>
13 <!-- Anything other than zero is an error -->
14 <exit_code range="1:" />
15 <exit_code range=":-1" />
16 </stdio>
17 <inputs>
18 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
19 <param name="module" type="select" display="radio" label="Classification module">
20 <options from_file="effectiveT3.loc">
21 <column name="value" index="0"/>
22 <column name="name" index="1"/>
23 <column name="path" index="2"/>
24 </options>
25 </param>
26 <conditional name="restrict">
27 <param name="type" type="select" label="Cut-off setting">
28 <option value="selective">Selective (threshold set in module)</option>
29 <option value="sensitive">Sensitive (threshold set in module)</option>
30 <option value="cutoff">User defined cut-off</option>
31 </param>
32 <when value="selective" />
33 <when value="sensitive" />
34 <when value="cutoff" >
35 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" />
36 </when>
37 </conditional>
38 </inputs>
39 <outputs>
40 <data name="tabular_file" format="tabular" label="$module.value_label results" />
41 </outputs>
42 <tests>
43 <test>
44 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
45 <param name="module" value="animal" />
46 <param name="type" value="selective" />
47 <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" />
48 </test>
49 <test>
50 <param name="fasta_file" value="empty.fasta" ftype="fasta" />
51 <param name="module" value="plant" />
52 <param name="type" value="sensistive" />
53 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
54 </test>
55 </tests>
56 <help>
57
58 **What it does**
59
60 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.
61
62 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):
63
64 ====== ==============================================================================
65 Column Description
66 ------ ------------------------------------------------------------------------------
67 1 Sequence identifier
68 2 Sequence description (from the FASTA file)
69 3 Score (between 0 and 1, or negative for an error such as a very short peptide)
70 4 Predicted effector (true/false)
71 ====== ==============================================================================
72
73
74 **References**
75
76 Jehl, Arnold and Rattei.
77 Effective - a database of predicted secreted bacterial proteins
78 Nucleic Acids Research, 39(Database issue), D591-5, 2011.
79 http://dx.doi.org/10.1093/nar/gkq1154
80
81 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
82 Sequence-based prediction of type III secreted proteins.
83 PLoS Pathog. 5(4):e1000376, 2009.
84 http://dx.doi.org/10.1371/journal.ppat.1000376
85
86 http://effectors.org/
87
88 </help>
89 </tool>