Mercurial > repos > peterjc > effectivet3

annotate tools/effectiveT3/effectiveT3.xml @ 10:a46d7861c32c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"Update all the pico_galaxy tools on main Tool Shed"
author peterjc
date Fri, 16 Apr 2021 22:34:56 +0000
parents 512530020360
children ed8c1babc166
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
a46d7861c32c "Update all the pico_galaxy tools on main Tool Shed"
peterjc
parents: 9
diff changeset
1 <tool id="effectiveT3" name="Effective T3" version="0.0.20">
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
2 <description>Find bacterial effectors in protein sequences</description>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
3 <requirements>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
4 <requirement type="package" version="1.0.1">effectiveT3</requirement>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
5 </requirements>
9
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
6 <version_command>
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
7 python $__tool_directory__/effectiveT3.py --version
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
8 </version_command>
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
9 <command detect_errors="aggressive">
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
10 python $__tool_directory__/effectiveT3.py '$module.fields.path'
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
11 #if $restrict.type=="cutoff":
9
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
12 'cutoff=$restrict.cutoff'
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
13 #else:
9
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
14 '$restrict.type'
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
15 #end if
9
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
16 '$fasta_file' '$tabular_file'
512530020360 v0.0.18 Internal changes to command line handling
peterjc
parents: 8
diff changeset
17 </command>
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
18 <inputs>
10
a46d7861c32c "Update all the pico_galaxy tools on main Tool Shed"
peterjc
parents: 9
diff changeset
19 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
20 <param name="module" type="select" display="radio" label="Classification module">
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
21 <options from_file="effectiveT3.loc">
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
22 <column name="value" index="0"/>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
23 <column name="name" index="1"/>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
24 <column name="path" index="2"/>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
25 </options>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
26 </param>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
27 <conditional name="restrict">
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
28 <param name="type" type="select" label="Cut-off setting">
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
29 <option value="selective">Selective (threshold set in module)</option>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
30 <option value="sensitive">Sensitive (threshold set in module)</option>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
31 <option value="cutoff">User defined cut-off</option>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
32 </param>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
33 <when value="selective" />
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
34 <when value="sensitive" />
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
35 <when value="cutoff" >
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
36 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" />
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
37 </when>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
38 </conditional>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
39 </inputs>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
40 <outputs>
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
41 <data name="tabular_file" format="tabular" label="Effective T3 $module.value_label on ${on_string}" />
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
42 </outputs>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
43 <tests>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
44 <test>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
45 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
46 <param name="module" value="animal" />
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
47 <param name="type" value="selective" />
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
48 <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" lines_diff="2"/>
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
49 </test>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
50 <test>
7
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
51 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
52 <param name="module" value="std_2_0_2" />
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
53 <param name="type" value="cutoff" />
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
54 <param name="cutoff" value="0.8" />
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
55 <output name="tabular_file" file="four_human_proteins.effectiveT3_std2.tabular" ftype="tabular" />
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
56 </test>
5f85301d50bf v0.0.16, adding new model TTSS-STD-2.0.2.jar
peterjc
parents: 6
diff changeset
57 <test>
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
58 <param name="fasta_file" value="empty.fasta" ftype="fasta" />
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
59 <param name="module" value="plant" />
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
60 <param name="type" value="sensitive" />
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
61 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
62 </test>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
63 </tests>
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
64 <help>
10
a46d7861c32c "Update all the pico_galaxy tools on main Tool Shed"
peterjc
parents: 9
diff changeset
65
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
66 **What it does**
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
67
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
68 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
69
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
70 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
71
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
72 ====== ==============================================================================
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
73 Column Description
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
74 ------ ------------------------------------------------------------------------------
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
75 1 Sequence identifier
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
76 2 Sequence description (from the FASTA file)
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
77 3 Score (between 0 and 1, or negative for an error such as a very short peptide)
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
78 4 Predicted effector (true/false)
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
79 ====== ==============================================================================
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
80
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
81
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
82 **References**
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
83
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
84 If you use this Galaxy tool in work leading to a scientific publication please
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
85 cite the following papers:
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
86
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
87 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
88 Galaxy tools and workflows for sequence analysis with applications
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
89 in molecular plant pathology. PeerJ 1:e167
10
a46d7861c32c "Update all the pico_galaxy tools on main Tool Shed"
peterjc
parents: 9
diff changeset
90 https://doi.org/10.7717/peerj.167
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
91
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
92 Jehl, Arnold and Rattei (2011).
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
93 Effective - a database of predicted secreted bacterial proteins
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
94 Nucleic Acids Research, 39(Database issue), D591-5.
10
a46d7861c32c "Update all the pico_galaxy tools on main Tool Shed"
peterjc
parents: 9
diff changeset
95 https://doi.org/10.1093/nar/gkq1154
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
96
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
97 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009).
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
98 Sequence-based prediction of type III secreted proteins.
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
99 PLoS Pathog. 5(4):e1000376.
10
a46d7861c32c "Update all the pico_galaxy tools on main Tool Shed"
peterjc
parents: 9
diff changeset
100 https://doi.org/10.1371/journal.ppat.1000376
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
101
4
f7ce32e13bc6 Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
peterjc
parents: 3
diff changeset
102 See also http://effectors.org/
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
103
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
104 This wrapper is available to install into other Galaxy Instances via the Galaxy
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
105 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
106 </help>
5
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
107 <citations>
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
108 <citation type="doi">10.7717/peerj.167</citation>
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
109 <citation type="doi">10.1093/nar/gkq1154</citation>
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
110 <citation type="doi">10.1371/journal.ppat.1000376</citation>
1ea715da1879 Uploaded v0.0.13, embed citation, relax test for floating point differences
peterjc
parents: 4
diff changeset
111 </citations>
3
b0b927299aee Uploaded v0.0.11 with automatic dependency installation.
peterjc
parents:
diff changeset
112 </tool>