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comparison tools/effectiveT3/effectiveT3.xml @ 4:f7ce32e13bc6 draft

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Uploaded v0.0.12, more explicit output name, MIT licence, RST README, citation information, development moved to GitHub
author peterjc
date Wed, 18 Sep 2013 06:11:36 -0400
parents b0b927299aee
children 1ea715da1879
comparison
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3:b0b927299aee 4:f7ce32e13bc6
1 <tool id="effectiveT3" name="Effective T3" version="0.0.11"> 1 <tool id="effectiveT3" name="Effective T3" version="0.0.12">
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 interpreter="python">effectiveT3.py --version</version_command> 6 <version_command interpreter="python">effectiveT3.py --version</version_command>
38 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" /> 38 <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1" />
39 </when> 39 </when>
40 </conditional> 40 </conditional>
41 </inputs> 41 </inputs>
42 <outputs> 42 <outputs>
43 <data name="tabular_file" format="tabular" label="$module.value_label results" /> 43 <data name="tabular_file" format="tabular" label="Effective T3 $module.value_label on ${on_string}" />
44 </outputs> 44 </outputs>
45 <tests> 45 <tests>
46 <test> 46 <test>
47 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" /> 47 <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
48 <param name="module" value="animal" /> 48 <param name="module" value="animal" />
74 ====== ============================================================================== 74 ====== ==============================================================================
75 75
76 76
77 **References** 77 **References**
78 78
79 Jehl, Arnold and Rattei. 79 If you use this Galaxy tool in work leading to a scientific publication please
80 cite the following papers:
81
82 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
83 Galaxy tools and workflows for sequence analysis with applications
84 in molecular plant pathology. PeerJ 1:e167
85 http://dx.doi.org/10.7717/peerj.167
86
87 Jehl, Arnold and Rattei (2011).
80 Effective - a database of predicted secreted bacterial proteins 88 Effective - a database of predicted secreted bacterial proteins
81 Nucleic Acids Research, 39(Database issue), D591-5, 2011. 89 Nucleic Acids Research, 39(Database issue), D591-5.
82 http://dx.doi.org/10.1093/nar/gkq1154 90 http://dx.doi.org/10.1093/nar/gkq1154
83 91
84 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei. 92 Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei (2009).
85 Sequence-based prediction of type III secreted proteins. 93 Sequence-based prediction of type III secreted proteins.
86 PLoS Pathog. 5(4):e1000376, 2009. 94 PLoS Pathog. 5(4):e1000376.
87 http://dx.doi.org/10.1371/journal.ppat.1000376 95 http://dx.doi.org/10.1371/journal.ppat.1000376
88 96
89 http://effectors.org/ 97 See also http://effectors.org/
90 98
91 This wrapper is available to install into other Galaxy Instances via the Galaxy 99 This wrapper is available to install into other Galaxy Instances via the Galaxy
92 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 100 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
93 </help> 101 </help>
94 </tool> 102 </tool>