Mercurial > repos > peterjc > effectivet3

annotate tools/protein_analysis/effectiveT3.xml @ 1:7479dbb285b5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.10, adds unit test
author peterjc
date Wed, 17 Apr 2013 05:25:25 -0400
parents 096088373590
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
1 <tool id="effectiveT3" name="Effective T3" version="0.0.10">
0
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
2 <description>Find bacterial effectors in protein sequences</description>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
3 <command interpreter="python">
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
4 effectiveT3.py $module.fields.path
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
5 #if $restrict.type=="cutoff":
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
6 cutoff=$restrict.cutoff
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
7 #else:
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
8 $restrict.type
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
9 #end if
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
10 $fasta_file $tabular_file</command>
1
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
11 <stdio>
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
12 <!-- Anything other than zero is an error -->
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
13 <exit_code range="1:" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
14 <exit_code range=":-1" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
15 </stdio>
0
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 <inputs>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
17 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18 <param name="module" type="select" display="radio" label="Classification module">
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
19 <options from_file="effectiveT3.loc">
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
20 <column name="value" index="0"/>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
21 <column name="name" index="1"/>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
22 <column name="path" index="2"/>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
23 </options>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 </param>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25 <conditional name="restrict">
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26 <param name="type" type="select" label="Cut-off setting">
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
27 <option value="selective">Selective (threshold set in module)</option>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
28 <option value="sensitive">Sensitive (threshold set in module)</option>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
29 <option value="cutoff">User defined cut-off</option>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30 </param>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
31 <when value="selective" />
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
32 <when value="sensitive" />
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
33 <when value="cutoff" >
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
34 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" />
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
35 </when>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
36 </conditional>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
37 </inputs>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
38 <outputs>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
39 <data name="tabular_file" format="tabular" label="$module.value_label results" />
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
40 </outputs>
1
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
41 <tests>
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
42 <test>
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
43 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
44 <param name="module" value="animal" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
45 <param name="type" value="selective" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
46 <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
47 </test>
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
48 <test>
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
49 <param name="fasta_file" value="empty.fasta" ftype="fasta" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
50 <param name="module" value="plant" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
51 <param name="type" value="sensistive" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
52 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
53 </test>
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
54 </tests>
0
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
55 <help>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
57 **What it does**
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
58
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
61 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62
1
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
63 ====== ==============================================================================
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
64 Column Description
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
65 ------ ------------------------------------------------------------------------------
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
66 1 Sequence identifier
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
67 2 Sequence description (from the FASTA file)
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
68 3 Score (between 0 and 1, or negative for an error such as a very short peptide)
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
69 4 Predicted effector (true/false)
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
70 ====== ==============================================================================
7479dbb285b5 Uploaded v0.0.10, adds unit test
peterjc
parents: 0
diff changeset
71
0
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
72
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
73 **References**
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75 Jehl, Arnold and Rattei.
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
76 Effective - a database of predicted secreted bacterial proteins
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
77 Nucleic Acids Research, 39(Database issue), D591-5, 2011.
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
78 http://dx.doi.org/10.1093/nar/gkq1154
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
79
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
81 Sequence-based prediction of type III secreted proteins.
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
82 PLoS Pathog. 5(4):e1000376, 2009.
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
83 http://dx.doi.org/10.1371/journal.ppat.1000376
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
84
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
85 http://effectors.org/
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
86
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
87 </help>
096088373590 Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
88 </tool>