Mercurial > repos > greg > assembly_post_processor

comparison macros.xml @ 37:cc4dba9f6ecd draft

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author greg
date Fri, 07 Apr 2017 08:34:58 -0400
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36:2553e8e46fab 37:cc4dba9f6ecd
1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros>
3 <xml name="requirements_assembly_post_processor">
4 <requirements>
5 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
6 </requirements>
7 </xml>
8 <xml name="requirements_gene_family_classifier">
9 <requirements>
10 <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
11 </requirements>
12 </xml>
13 <xml name="requirements_gene_family_integrator">
14 <requirements>
15 <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
16 </requirements>
17 </xml>
18 <xml name="stdio">
19 <stdio>
20 <exit_code range="1:"/>
21 <exit_code range=":-1"/>
22 <regex match="Error:"/>
23 <regex match="Exception:"/>
24 </stdio>
25 </xml>
26 <xml name="param_scaffold">
27 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
28 <options from_data_table="plant_tribes_scaffolds" />
29 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
30 </param>
31 </xml>
32 <xml name="param_method">
33 <param name="method" type="select" label="Protein clustering method">
34 <option value="gfam" selected="true">GFam</option>
35 <option value="orthofinder">OrthoFinder</option>
36 <option value="orthomcl">OrthoMCL</option>
37 </param>
38 </xml>
39 <xml name="param_orthogroup_fna">
40 <param name="orthogroup_fna" type="select" display="radio" label="Process corresponding gene family classification orthogroups CDS fasta files?">
41 <option value="yes" selected="true">Yes</option>
42 <option value="no">No</option>
43 </param>
44 </xml>
45 <xml name="citation1">
46 <citation type="bibtex">
47 @misc{None,
48 journal = {None},
49 author = {1. Wafula EK},
50 title = {Manuscript in preparation},
51 year = {None},
52 url = {https://github.com/dePamphilis/PlantTribes},}
53 </citation>
54 </xml>
55 <xml name="citations2to4">
56 <citation type="bibtex">
57 @article{Sasidharan2012,
58 journal = {Nucleic Acids Research},
59 author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
60 title = {GFam: a platform for automatic annotation of gene families},
61 year = {2012},
62 pages = {gks631},}
63 </citation>
64 <citation type="bibtex">
65 @article{Li2003,
66 journal = {Genome Research}
67 author = {3. Li L, Stoeckert CJ, Roos DS},
68 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
69 year = {2003},
70 volume = {13},
71 number = {9},
72 pages = {2178-2189},}
73 </citation>
74 <citation type="bibtex">
75 @article{Emms2015,
76 journal = {Genome Biology}
77 author = {4. Emms DM, Kelly S},
78 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
79 year = {2015},
80 volume = {16},
81 number = {1},
82 pages = {157},}
83 </citation>
84 </xml>
85 </macros>