Mercurial > repos > greg > gene_family_integrator

comparison macros.xml @ 5:077f036ca17d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 07 Apr 2017 16:30:51 -0400
parents 109a0eb7791f
children 1d178e90fbe6
comparison
equal deleted inserted replaced
4:9fff0561bc8e 5:077f036ca17d
3 <xml name="requirements_assembly_post_processor"> 3 <xml name="requirements_assembly_post_processor">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement> 5 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
6 </requirements> 6 </requirements>
7 </xml> 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>
8 <xml name="requirements_gene_family_classifier"> 13 <xml name="requirements_gene_family_classifier">
9 <requirements> 14 <requirements>
10 <requirement type="package" version="0.4">plant_tribes_gene_family_classifier</requirement> 15 <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
11 </requirements> 16 </requirements>
12 </xml> 17 </xml>
13 <xml name="requirements_gene_family_integrator"> 18 <xml name="requirements_gene_family_integrator">
14 <requirements> 19 <requirements>
15 <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement> 20 <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
21 </requirements>
22 </xml>
23 <xml name="requirements_kaks_analysis">
24 <requirements>
25 <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
16 </requirements> 26 </requirements>
17 </xml> 27 </xml>
18 <xml name="stdio"> 28 <xml name="stdio">
19 <stdio> 29 <stdio>
20 <exit_code range="1:"/> 30 <exit_code range="1:"/>
21 <exit_code range=":-1"/> 31 <exit_code range=":-1"/>
22 <regex match="Error:"/> 32 <regex match="Error:"/>
23 <regex match="Exception:"/> 33 <regex match="Exception:"/>
24 </stdio> 34 </stdio>
25 </xml> 35 </xml>
26 <xml name="param_scaffold"> 36 <xml name="param_codon_alignments">
27 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 37 <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
28 <options from_data_table="plant_tribes_scaffolds" /> 38 <option value="yes" selected="true">Yes</option>
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." /> 39 <option value="no">No</option>
30 </param> 40 </param>
31 </xml> 41 </xml>
32 <xml name="param_method"> 42 <xml name="param_method">
33 <param name="method" type="select" label="Protein clustering method"> 43 <param name="method" type="select" label="Protein clustering method">
34 <option value="gfam" selected="true">GFam</option> 44 <option value="gfam" selected="true">GFam</option>
35 <option value="orthofinder">OrthoFinder</option> 45 <option value="orthofinder">OrthoFinder</option>
36 <option value="orthomcl">OrthoMCL</option> 46 <option value="orthomcl">OrthoMCL</option>
37 </param> 47 </param>
38 </xml> 48 </xml>
49 <xml name="param_options_type">
50 <param name="options_type" type="select" label="Options Configuration">
51 <option value="basic" selected="true">Basic</option>
52 <option value="advanced">Advanced</option>
53 </param>
54 </xml>
39 <xml name="param_orthogroup_fna"> 55 <xml name="param_orthogroup_fna">
40 <param name="orthogroup_fna" type="select" display="radio" label="Process corresponding gene family classification orthogroups CDS fasta files?"> 56 <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
41 <option value="yes" selected="true">Yes</option> 57 <option value="yes" selected="true">Yes</option>
42 <option value="no">No</option> 58 <option value="no">No</option>
43 </param> 59 </param>
60 </xml>
61 <xml name="param_scaffold">
62 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
63 <options from_data_table="plant_tribes_scaffolds" />
64 <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." />
65 </param>
66 </xml>
67 <xml name="cond_alignment_method">
68 <conditional name="alignment_method_cond">
69 <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
70 <option value="mafft" selected="true">MAFFT algorithm</option>
71 <option value="pasta">PASTA algorithm</option>
72 </param>
73 <when value="mafft" />
74 <when value="pasta">
75 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
76 </when>
77 </conditional>
78 </xml>
79 <xml name="cond_remove_gappy_sequences">
80 <conditional name="remove_gappy_sequences_cond">
81 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
82 <option value="no" selected="true">No</option>
83 <option value="yes">Yes</option>
84 </param>
85 <when value="no" />
86 <when value="yes">
87 <conditional name="trim_type_cond">
88 <param name="trim_type" type="select" label="Select process used for gap trimming">
89 <option value="gap_trimming" selected="true">Nucleotide based </option>
90 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
91 </param>
92 <when value="gap_trimming">
93 <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" />
94 </when>
95 <when value="automated_trimming" />
96 </conditional>
97 <conditional name="remove_sequences_with_gaps_cond">
98 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
99 <option value="no" selected="true">No</option>
100 <option value="yes">Yes</option>
101 </param>
102 <when value="no" />
103 <when value="yes">
104 <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" />
105 <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
106 </when>
107 </conditional>
108 </when>
109 </conditional>
44 </xml> 110 </xml>
45 <xml name="citation1"> 111 <xml name="citation1">
46 <citation type="bibtex"> 112 <citation type="bibtex">
47 @misc{None, 113 @misc{None,
48 journal = {None}, 114 journal = {None},