Mercurial > repos > greg > assembly_post_processor

comparison macros.xml @ 39:b0ea1e985a38 draft

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author greg
date Wed, 26 Apr 2017 10:25:55 -0400
parents cc4dba9f6ecd
children 8102c8bf2414
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38:9b5baf12bdbe 39:b0ea1e985a38
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros> 2 <macros>
3 <token name="@WRAPPER_VERSION@">0.8</token>
3 <xml name="requirements_assembly_post_processor"> 4 <xml name="requirements_assembly_post_processor">
4 <requirements> 5 <requirements>
5 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement> 6 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
7 </requirements>
8 </xml>
9 <xml name="requirements_gene_family_aligner">
10 <requirements>
11 <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement>
6 </requirements> 12 </requirements>
7 </xml> 13 </xml>
8 <xml name="requirements_gene_family_classifier"> 14 <xml name="requirements_gene_family_classifier">
9 <requirements> 15 <requirements>
10 <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement> 16 <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
13 <xml name="requirements_gene_family_integrator"> 19 <xml name="requirements_gene_family_integrator">
14 <requirements> 20 <requirements>
15 <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement> 21 <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
16 </requirements> 22 </requirements>
17 </xml> 23 </xml>
24 <xml name="requirements_kaks_analysis">
25 <requirements>
26 <requirement type="package" version="0.8">plant_tribes_kaks_analysis</requirement>
27 </requirements>
28 </xml>
29 <xml name="requirements_gene_family_phylogeny_builder">
30 <requirements>
31 <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
32 </requirements>
33 </xml>
18 <xml name="stdio"> 34 <xml name="stdio">
19 <stdio> 35 <stdio>
20 <exit_code range="1:"/> 36 <exit_code range="1:"/>
21 <exit_code range=":-1"/> 37 <exit_code range=":-1"/>
22 <regex match="Error:"/> 38 <regex match="Error:"/>
23 <regex match="Exception:"/> 39 <regex match="Exception:"/>
24 </stdio> 40 </stdio>
25 </xml> 41 </xml>
26 <xml name="param_scaffold"> 42 <xml name="param_codon_alignments">
27 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 43 <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
28 <options from_data_table="plant_tribes_scaffolds" /> 44 <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." /> 45 <option value="no">No</option>
30 </param> 46 </param>
31 </xml> 47 </xml>
32 <xml name="param_method"> 48 <xml name="param_method">
33 <param name="method" type="select" label="Protein clustering method"> 49 <param name="method" type="select" label="Protein clustering method">
34 <option value="gfam" selected="true">GFam</option> 50 <option value="gfam" selected="true">GFam</option>
35 <option value="orthofinder">OrthoFinder</option> 51 <option value="orthofinder">OrthoFinder</option>
36 <option value="orthomcl">OrthoMCL</option> 52 <option value="orthomcl">OrthoMCL</option>
37 </param> 53 </param>
38 </xml> 54 </xml>
55 <xml name="param_options_type">
56 <param name="options_type" type="select" label="Options Configuration">
57 <option value="basic" selected="true">Basic</option>
58 <option value="advanced">Advanced</option>
59 </param>
60 </xml>
39 <xml name="param_orthogroup_fna"> 61 <xml name="param_orthogroup_fna">
40 <param name="orthogroup_fna" type="select" display="radio" label="Process corresponding gene family classification orthogroups CDS fasta files?"> 62 <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
41 <option value="yes" selected="true">Yes</option> 63 <option value="yes" selected="true">Yes</option>
42 <option value="no">No</option> 64 <option value="no">No</option>
43 </param> 65 </param>
66 </xml>
67 <xml name="param_scaffold">
68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
69 <options from_data_table="plant_tribes_scaffolds" />
70 <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." />
71 </param>
72 </xml>
73 <xml name="param_sequence_type">
74 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
75 <option value="protein" selected="true">Amino acid based</option>
76 <option value="dna">Nucleotide based</option>
77 </param>
78 </xml>
79 <xml name="cond_alignment_method">
80 <conditional name="alignment_method_cond">
81 <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
82 <option value="mafft" selected="true">MAFFT algorithm</option>
83 <option value="pasta">PASTA algorithm</option>
84 </param>
85 <when value="mafft" />
86 <when value="pasta">
87 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
88 </when>
89 </conditional>
90 </xml>
91 <xml name="cond_remove_gappy_sequences">
92 <conditional name="remove_gappy_sequences_cond">
93 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
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 <conditional name="trim_type_cond">
100 <param name="trim_type" type="select" label="Select process used for trimming">
101 <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option>
102 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option>
103 </param>
104 <when value="gap_trimming">
105 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Remove sites in alignments with gaps of" />
106 </when>
107 <when value="automated_trimming" />
108 </conditional>
109 <conditional name="remove_sequences_with_gaps_cond">
110 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
111 <option value="no" selected="true">No</option>
112 <option value="yes">Yes</option>
113 </param>
114 <when value="no" />
115 <when value="yes">
116 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Remove sequences with gaps of" />
117 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Maximum number of iterations" />
118 </when>
119 </conditional>
120 </when>
121 </conditional>
44 </xml> 122 </xml>
45 <xml name="citation1"> 123 <xml name="citation1">
46 <citation type="bibtex"> 124 <citation type="bibtex">
47 @misc{None, 125 @misc{None,
48 journal = {None}, 126 journal = {None},