Mercurial > repos > peterjc > effectivet3

comparison 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
comparison
equal deleted inserted replaced
9:512530020360 10:a46d7861c32c
1 <tool id="effectiveT3" name="Effective T3" version="0.0.18"> 1 <tool id="effectiveT3" name="Effective T3" version="0.0.20">
2 <description>Find bacterial effectors in protein sequences</description> 2 <description>Find bacterial effectors in protein sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.0.1">effectiveT3</requirement> 4 <requirement type="package" version="1.0.1">effectiveT3</requirement>
5 </requirements> 5 </requirements>
6 <version_command> 6 <version_command>
14 '$restrict.type' 14 '$restrict.type'
15 #end if 15 #end if
16 '$fasta_file' '$tabular_file' 16 '$fasta_file' '$tabular_file'
17 </command> 17 </command>
18 <inputs> 18 <inputs>
19 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 19 <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/>
20 <param name="module" type="select" display="radio" label="Classification module"> 20 <param name="module" type="select" display="radio" label="Classification module">
21 <options from_file="effectiveT3.loc"> 21 <options from_file="effectiveT3.loc">
22 <column name="value" index="0"/> 22 <column name="value" index="0"/>
23 <column name="name" index="1"/> 23 <column name="name" index="1"/>
24 <column name="path" index="2"/> 24 <column name="path" index="2"/>
60 <param name="type" value="sensitive" /> 60 <param name="type" value="sensitive" />
61 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" /> 61 <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
62 </test> 62 </test>
63 </tests> 63 </tests>
64 <help> 64 <help>
65 65
66 **What it does** 66 **What it does**
67 67
68 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins. 68 This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.
69 69
70 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein): 70 The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):
85 cite the following papers: 85 cite the following papers:
86 86
87 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). 87 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
88 Galaxy tools and workflows for sequence analysis with applications 88 Galaxy tools and workflows for sequence analysis with applications
89 in molecular plant pathology. PeerJ 1:e167 89 in molecular plant pathology. PeerJ 1:e167
90 http://dx.doi.org/10.7717/peerj.167 90 https://doi.org/10.7717/peerj.167
91 91
92 Jehl, Arnold and Rattei (2011). 92 Jehl, Arnold and Rattei (2011).
93 Effective - a database of predicted secreted bacterial proteins 93 Effective - a database of predicted secreted bacterial proteins
94 Nucleic Acids Research, 39(Database issue), D591-5. 94 Nucleic Acids Research, 39(Database issue), D591-5.
95 http://dx.doi.org/10.1093/nar/gkq1154 95 https://doi.org/10.1093/nar/gkq1154
96 96
97 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009). 97 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009).
98 Sequence-based prediction of type III secreted proteins. 98 Sequence-based prediction of type III secreted proteins.
99 PLoS Pathog. 5(4):e1000376. 99 PLoS Pathog. 5(4):e1000376.
100 http://dx.doi.org/10.1371/journal.ppat.1000376 100 https://doi.org/10.1371/journal.ppat.1000376
101 101
102 See also http://effectors.org/ 102 See also http://effectors.org/
103 103
104 This wrapper is available to install into other Galaxy Instances via the Galaxy 104 This wrapper is available to install into other Galaxy Instances via the Galaxy
105 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 105 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3