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comparison macros.xml @ 0:6accbd3a1449 draft

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author greg
date Fri, 07 Apr 2017 13:00:29 -0400
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-1:000000000000 0:6accbd3a1449
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_aligner">
9 <requirements>
10 <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement>
11 </requirements>
12 </xml>
13 <xml name="requirements_gene_family_classifier">
14 <requirements>
15 <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
16 </requirements>
17 </xml>
18 <xml name="requirements_gene_family_integrator">
19 <requirements>
20 <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
21 </requirements>
22 </xml>
23 <xml name="stdio">
24 <stdio>
25 <exit_code range="1:"/>
26 <exit_code range=":-1"/>
27 <regex match="Error:"/>
28 <regex match="Exception:"/>
29 </stdio>
30 </xml>
31 <xml name="param_codon_alignments">
32 <param name="codon_alignments" type="select" display="radio" label="Construct orthogroup multiple codon alignments?">
33 <option value="yes" selected="true">Yes</option>
34 <option value="no">No</option>
35 </param>
36 </xml>
37 <xml name="param_method">
38 <param name="method" type="select" label="Protein clustering method">
39 <option value="gfam" selected="true">GFam</option>
40 <option value="orthofinder">OrthoFinder</option>
41 <option value="orthomcl">OrthoMCL</option>
42 </param>
43 </xml>
44 <xml name="param_options_type">
45 <param name="options_type" type="select" label="Options Configuration">
46 <option value="basic" selected="true">Basic</option>
47 <option value="advanced">Advanced</option>
48 </param>
49 </xml>
50 <xml name="param_orthogroup_fna">
51 <param name="orthogroup_fna" type="select" display="radio" label="Process corresponding gene family classification orthogroups CDS fasta files?">
52 <option value="yes" selected="true">Yes</option>
53 <option value="no">No</option>
54 </param>
55 </xml>
56 <xml name="param_scaffold">
57 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
58 <options from_data_table="plant_tribes_scaffolds" />
59 <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." />
60 </param>
61 </xml>
62 <xml name="cond_alignment_method">
63 <conditional name="alignment_method_cond">
64 <param name="alignments_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
65 <option value="mafft" selected="true">MAFFT algorithm</option>
66 <option value="pasta">PASTA algorithm</option>
67 </param>
68 <when value="mafft" />
69 <when value="pasta">
70 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
71 </when>
72 </conditional>
73 </xml>
74 <xml name="cond_remove_gappy_sequences">
75 <conditional name="remove_gappy_sequences_cond">
76 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
77 <option value="no" selected="true">No</option>
78 <option value="yes">Yes</option>
79 </param>
80 <when value="no" />
81 <when value="yes">
82 <conditional name="trim_type_cond">
83 <param name="trim_type" type="select" label="Select process used for gap trimming">
84 <option value="gap_trimming" selected="true">Nucleotide based </option>
85 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
86 </param>
87 <when value="gap_trimming">
88 <param name="gap_trimming" type="float" value="0" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="Zero value has no affect" />
89 </when>
90 <when value="automated_trimming" />
91 </conditional>
92 <conditional name="remove_sequences_with_gaps_cond">
93 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
94 <option value="no" selected="true">No</option>
95 <option value="yes">Yes</option>
96 </param>
97 <when value="no" />
98 <when value="yes">
99 <param name="remove_sequences_with_gaps_of" type="float" value="0" min="0" max="1" label="Remove sequences with gaps of" help="Zero value has no affect" />
100 <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
101 </when>
102 </conditional>
103 </when>
104 </conditional>
105 </xml>
106 <xml name="citation1">
107 <citation type="bibtex">
108 @misc{None,
109 journal = {None},
110 author = {1. Wafula EK},
111 title = {Manuscript in preparation},
112 year = {None},
113 url = {https://github.com/dePamphilis/PlantTribes},}
114 </citation>
115 </xml>
116 <xml name="citations2to4">
117 <citation type="bibtex">
118 @article{Sasidharan2012,
119 journal = {Nucleic Acids Research},
120 author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
121 title = {GFam: a platform for automatic annotation of gene families},
122 year = {2012},
123 pages = {gks631},}
124 </citation>
125 <citation type="bibtex">
126 @article{Li2003,
127 journal = {Genome Research}
128 author = {3. Li L, Stoeckert CJ, Roos DS},
129 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
130 year = {2003},
131 volume = {13},
132 number = {9},
133 pages = {2178-2189},}
134 </citation>
135 <citation type="bibtex">
136 @article{Emms2015,
137 journal = {Genome Biology}
138 author = {4. Emms DM, Kelly S},
139 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
140 year = {2015},
141 volume = {16},
142 number = {1},
143 pages = {157},}
144 </citation>
145 </xml>
146 </macros>