Mercurial > repos > dereeper > blup_calculator
comparison blupcal.xml @ 0:45d215f2be74 draft
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author | dereeper |
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date | Sat, 29 Dec 2018 18:44:05 -0500 |
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children | c1c85170db1b |
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1 <tool id="blup_and_blue_multiple2" name="BLUP/BLUE" version="1.11.0"> | |
2 <description>calculator (multiple traits)</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.1_18_1">r-lme4</requirement> | |
5 <requirement type="package" version="1.20.2">r-getopt</requirement> | |
6 </requirements> | |
7 <command interpreter="bash"> | |
8 ./blupcal.sh $__tool_directory__ $galaxy_tabular_file $galaxy_replication_vector_column_index $galaxy_genotype_vector_column_index $galaxy_first_y_vector_column_index $galaxy_last_y_vector_column_index $galaxy_design_conditional.galaxy_design | |
9 $galaxy_summarize_by | |
10 $galaxy_summarize_by_vector_column_index | |
11 $galaxy_group_variable_1 | |
12 $galaxy_group_variable_1_vector_column_index | |
13 $galaxy_group_variable_2 | |
14 $galaxy_group_variable_2_vector_column_index | |
15 $galaxy_output_file_path | |
16 #if $galaxy_design_conditional.galaxy_design == "lattice": | |
17 $galaxy_design_conditional.galaxy_block_vector_column_index | |
18 #else: | |
19 NULL | |
20 #end if | |
21 </command> | |
22 <inputs> | |
23 <param name="galaxy_tabular_file" | |
24 type="data" | |
25 format="tab,tabular" | |
26 label="Encoded Data" | |
27 help="(required) Must be the TAB as both column delimiter and file type" /> | |
28 <conditional name="galaxy_design_conditional"> | |
29 <param name="galaxy_design" | |
30 type="select" | |
31 label="Design" | |
32 help="(required) Must choose one of the two design options available: Lattice or RCBD"> | |
33 <option value="lattice">Lattice</option> | |
34 <option value="rcbd" | |
35 selected="true">RCBD</option> | |
36 </param> | |
37 <when value="lattice"> | |
38 <param name="galaxy_block_vector_column_index" | |
39 type="data_column" | |
40 data_ref="galaxy_tabular_file" | |
41 use_header_names="true" | |
42 label="Block within Replication" | |
43 help="(required) Must be the block-vector column name" | |
44 value="4" /> | |
45 </when> | |
46 <when value="rcbd"> | |
47 </when> | |
48 </conditional> | |
49 <param name="galaxy_replication_vector_column_index" | |
50 type="data_column" | |
51 data_ref="galaxy_tabular_file" | |
52 use_header_names="true" | |
53 label="Replication Column" | |
54 help="(required) Must be the replication-vector column name" | |
55 value="1" /> | |
56 <param name="galaxy_genotype_vector_column_index" | |
57 type="data_column" | |
58 data_ref="galaxy_tabular_file" | |
59 use_header_names="true" | |
60 label="Genotype Column" | |
61 help="(required) Must be the genotype-vector column name" | |
62 value="2" /> | |
63 <param name="galaxy_first_y_vector_column_index" | |
64 type="data_column" | |
65 data_ref="galaxy_tabular_file" | |
66 use_header_names="true" | |
67 label="First Y Column" | |
68 help="(required) Must be the first y-vector column name" | |
69 value="3" /> | |
70 <param name="galaxy_last_y_vector_column_index" | |
71 type="data_column" | |
72 data_ref="galaxy_tabular_file" | |
73 use_header_names="true" | |
74 label="Last Y Column" | |
75 help="(required) Must be the last y-vector column name" | |
76 value="3" /> | |
77 <param name="galaxy_summarize_by" | |
78 type="boolean" | |
79 checked="false" | |
80 truevalue="true" | |
81 falsevalue="false" | |
82 label="Summarize By" | |
83 help="(optional) It can be summarized by a column chosen" /> | |
84 <param name="galaxy_summarize_by_vector_column_index" | |
85 type="data_column" | |
86 data_ref="galaxy_tabular_file" | |
87 use_header_names="true" | |
88 label="Summarize By Column" | |
89 help="Must be the summarized-vector column name" | |
90 value="5" /> | |
91 <param name="galaxy_group_variable_1" | |
92 type="boolean" | |
93 checked="false" | |
94 truevalue="true" | |
95 falsevalue="false" | |
96 label="Variable 1, Factor" | |
97 help="(optional) It can choose any column as the group variable 1" /> | |
98 <param name="galaxy_group_variable_1_vector_column_index" | |
99 type="data_column" | |
100 data_ref="galaxy_tabular_file" | |
101 use_header_names="true" | |
102 label="Variable 1, Factor Column" | |
103 help="Must be the group-variable-1-vector column name" | |
104 value="6" /> | |
105 <param name="galaxy_group_variable_2" | |
106 type="boolean" | |
107 checked="false" | |
108 truevalue="true" | |
109 falsevalue="false" | |
110 label="Variable 2, Factor" | |
111 help="(optional) It can choose any column as the group variable 2" /> | |
112 <param name="galaxy_group_variable_2_vector_column_index" | |
113 type="data_column" | |
114 data_ref="galaxy_tabular_file" | |
115 use_header_names="true" | |
116 label="Variable 2, Factor Column" | |
117 help="Must be the group-variable-2-vector column name" | |
118 value="7" /> | |
119 </inputs> | |
120 <outputs> | |
121 <data name="galaxy_output_file_path" | |
122 format="tab" | |
123 label="BLUP output data" /> | |
124 </outputs> | |
125 <tests> | |
126 <test> | |
127 <param name="galaxy_tabular_file" value="pheno_input.tab.txt" /> | |
128 <param name="galaxy_replication_vector_column_index" value="1" /> | |
129 <param name="galaxy_genotype_vector_column_index" value="18" /> | |
130 <param name="galaxy_first_y_vector_column_index" value="13" /> | |
131 <param name="galaxy_last_y_vector_column_index" value="14" /> | |
132 <param name="galaxy_summarize_by" value="true" /> | |
133 <param name="galaxy_summarize_by_vector_column_index" value="3" /> | |
134 <output name="galaxy_output_file_path" file="blup.output" compare="sim_size" > | |
135 <assert_contents> | |
136 <has_n_columns n="12" /> | |
137 </assert_contents> | |
138 </output> | |
139 </test> | |
140 </tests> | |
141 <help> | |
142 **What it does** | |
143 | |
144 This function calculates BLUP, BLUE and means for Y variable based on the model specified by the user. | |
145 | |
146 The required variables for RCBD are Genotype and Replication and for lattice required variables are Genotype, Replication (main block) and Block within Replication (sub block or block). User can add additional two X variables (eg. Location, Season etc) in the model and are treated as factor ( even supplied as numerical variable). | |
147 If you want to calculate BLUP / BLUE by a grouping variable (eg. Management), then this will calculate BLUP / BLUE for each level of the variable. | |
148 | |
149 **Model** | |
150 | |
151 for RCBD design | |
152 | |
153 without additional factors (variable 1 and variable 2) | |
154 | |
155 *Y = Genotype + Replication + error* RCBD | |
156 | |
157 *Y = Genotype + Replication + Block within Replication + error* Lattice | |
158 | |
159 | |
160 With variable 1 | |
161 | |
162 *Y = Variable 1 + Genotype + Variable 1 : Genotype + Replication + error* RCBD | |
163 | |
164 *Y = Variable 1 + Genotype + Replication + Variable 1 : Genotype + Block within Replication + error* Lattice | |
165 | |
166 | |
167 With variable 1 and variable 2 | |
168 | |
169 *Y = Variable 2 + Variable 1 + Genotype + Variable 1 : Genotype + Variable 1: Variable 2 + Variable 1:Variable 2: Genotype + Replication + error* RCBD | |
170 *Y = Variable 2 + Variable 1 + Genotype + Variable 1 : Genotype + Variable 1: Variable 2 + Variable 1:Variable 2: Genotype + Replication + Block within Replication + error* RCBD | |
171 | |
172 **Model details** | |
173 | |
174 - Genotype is treated as Fixed for BLUE calculation and random for BLUP calculation. | |
175 - Replication, Block within Replication are treated as random both BLUP and BLUE calculations. | |
176 - Variable 1, Genotype : Variable 1 are treated as random both BLUP and BLUE calculations. | |
177 - Variable 2, Genotype : Variable 2, Variable 1 : Variable 2, Genotype : Variable 1 : Variable 2 are treated as random effects for both BLUP and BLUE calculations. | |
178 | |
179 | |
180 **Citation** | |
181 Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48. | |
182 | |
183 **Author(s)** | |
184 </help> | |
185 </tool> |