annotate aurora_wgcna.xml @ 4:b14e4bf568b0 draft

Uploaded
author spficklin
date Mon, 25 Nov 2019 12:17:08 -0500
parents c18d0db68d51
children 1915371bea02
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
1 <tool id="aurora_wgcna" name="Aurora Galaxy WGCNA" version="1.0.0">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
2 <description>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
3 Identify gene co-expression network modules using WGCNA.
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
4 </description>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
5 <requirements>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
6 <requirement type="package" version="2.7.3">pandoc</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
7 <requirement type="package" version="1.20.3">r-getopt</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
8 <requirement type="package" version="1.12">r-rmarkdown</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
9 <requirement type="package" version="1.8.4">r-plyr</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
10 <requirement type="package" version="0.10">r-dt</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
11 <requirement type="package" version="0.4.0">r-htmltools</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
12 <requirement type="package" version="3.2.1">r-ggplot2</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
13 <requirement type="package" version="1.4.3">r-reshape2</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
14 <requirement type="package" version="6.0_83">r-caret</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
15 <requirement type="package" version="1.68">r-wgcna</requirement>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
16 </requirements>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
17 <stdio>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
18 <regex match="Execution halted"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
19 source="both"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
20 level="fatal"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
21 description="Execution halted." />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
22 <regex match="Error in"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
23 source="both"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
24 level="fatal"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
25 description="An undefined error occured, please check your intput carefully and contact your administrator." />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
26 <regex match="Fatal error"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
27 source="both"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
28 level="fatal"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
29 description="An undefined error occured, please check your intput carefully and contact your administrator." />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
30 </stdio>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
31 <command>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
32 <![CDATA[
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
33 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
34
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
35 Rscript '${__tool_directory__}/aurora_wgcna_render.R'
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
36 -e $expression_data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
37 -s $min_cluster_size
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
38 -b $block_size
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
39 -j $hard_threshold
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
40 #if $trait_info.trait_data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
41 -t $trait_info.trait_data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
42 -c $trait_info.sname_col
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
43 #if $trait_info.missing_value2
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
44 -o "$trait_info.missing_value2"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
45 #else
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
46 -o "NA"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
47 #end if
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
48 #if $trait_info.one_hot_cols
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
49 -y $trait_info.one_hot_cols
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
50 #end if
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
51 #if $trait_info.ignore_cols
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
52 -x $trait_info.ignore_cols
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
53 #end if
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
54 #end if
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
55 #if $height_cut
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
56 -h $height_cut
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
57 #end if
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
58 #if $power
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
59 -p $power
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
60 #end if
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
61 -l $render_log_file
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
62 -a $r_data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
63 -k $gene_module_file
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
64 -w $network_edges_file
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
65 -g $gene_association_file
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
66 -m $module_association_file
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
67 -q $module_association_report
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
68 -r $network_construction_report
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
69 -z $updated_trait_matrix
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
70 -d $filtered_GEM
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
71 -i $missing_value1
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
72 ]]>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
73 </command>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
74 <inputs>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
75 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
76 type="data"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
77 name="expression_data"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
78 format="csv"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
79 optional="false"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
80 label="Gene expression data"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
81 help="The gene expression data is an n x m matrix where n rows are the genes, m columns are the samples and the elements represent gene expression levels (derived either from Microarray or RNA-Seq). The matrix should be stored in a comma-separated (CSV) file and it must have a header. The gene names must appear as the first column of data in the file."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
82 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
83 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
84 type="text"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
85 value="NA"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
86 name="missing_value1"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
87 optional="false"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
88 label="Missing Value Identifier"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
89 help="Within the gene expression data some genes may have missing values. If so, please indicate the text that is used to identify a missing value. Some common examples include: NA, 0.0, 0, -Inf. Any expression level that exactly matches the value provided will be considered a missing value."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
90 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
91 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
92 type="float"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
93 value=""
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
94 name="height_cut"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
95 optional="true"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
96 label="Outlier Dendrogram Cut Height"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
97 help="When checking for outliers, WGCNA performs hierarchical clustering. The resulting dendrogram can be cut at the given height to remove outliers. If no value is provided a cut height will automatically be determined. Try running this tool first without providing a value. Return and set a value if the results are not adequate."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
98 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
99 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
100 type="integer"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
101 value=""
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
102 name="power"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
103 optional="true"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
104 label="Power"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
105 help="Prior to network construction, WGCNA recommends that the gene expression data is raised to a power. The exact power that should be used will be automatically determined. Try running this tool first without providing a value. Return and set a value if the results are not adequate."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
106 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
107 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
108 type="integer"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
109 value="30"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
110 name="min_cluster_size"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
111 optional="false"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
112 label="Minimum Module Size"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
113 help="The minimum module size. Modules smaller than this will not be included in the network."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
114 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
115 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
116 type="integer"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
117 value="5000"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
118 min="1000"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
119 max="10000"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
120 name="block_size"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
121 optional="false"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
122 label="Block Size"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
123 help="Constructing a network can use an extreme amount of memory if the number of genes is high. The block size enables WGCNA to divide the data into blocks of genes with similar expression reducing the amount of memory used. The block size indicates the maximum number of genes that can be used in a block. The total number of blocks used will be the total genes divided by this number (plus 1 for any remainder)."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
124 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
125 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
126 type="float"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
127 value="0.5"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
128 name="hard_threshold"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
129 optional="false"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
130 label="Hard Threshold"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
131 min="0"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
132 max="1"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
133 help="While WGCNA uses a soft thresholding approach for finding modules and constructing gene similarity, when exporting the network for display as a graph a hard threshold is still required. For WGCNA, the threhshold is applied to the Euclidian distance between all genes. But, there is no set prescribed method to decide on a proper hard threshold value. Set a threshold now, then you can apply filters later (such as in Cytoscape) to remove low weighted edges if desired."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
134 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
135 <section name="trait_info" title="Trait/Phenotype" expanded="true">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
136 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
137 type="data"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
138 name="trait_data"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
139 format="csv"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
140 optional="true"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
141 label="Trait/Phenotype Data Matrix"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
142 help="The trait/phenotype data is an n x m matrix where n is the samples and m are the features such as experimental condition, biosample properties, traits or phenotype values. The matrix should be stored in a comma-separated (CSV) file. It must have a header."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
143 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
144 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
145 type="text"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
146 value="NA"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
147 name="missing_value2"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
148 optional="true"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
149 label="Missing Value Identifier"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
150 help="Within the trait data some columns may have missing values. If so, please indicate the text that is used to identify a missing value. Some common examples include: NA, 0.0, 0, -Inf. Any value that exactly matches the value provided will be considered a missing value."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
151 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
152 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
153 type="integer"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
154 value="1"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
155 name="sname_col"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
156 optional="true"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
157 label="Sample Name Column"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
158 help="The number of the column (starting from 1) in the sample annotation data file where the sample name column is found."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
159 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
160 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
161 type="text"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
162 value=""
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
163 name="one_hot_cols"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
164 optional="true"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
165 label="Categorical Columns"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
166 help="Categorical columns in the sample daa matrix must be '1-hot encoded'. This means that each categorical column is expanded into new columns (one for each category) and the values for the new columns are set to 1 if the sample has the category and 0 if not. This value should be a comma-separated list of column names with no spaces between column names. Please make sure the column headers only have alphanumeric characters and underscores. If you do not specify categorical column names then they will be converted to factors and treated as ordinal data."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
167 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
168 <param
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
169 type="text"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
170 value=""
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
171 name="ignore_cols"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
172 optional="true"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
173 label="Columns to Ignore"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
174 help="The names of columns in the sample data matrix that should be ignored. This value should be a comma-separated list of column names with no spaces between column names. Please make sure the column headers only have alphanumeric characters and underscores."
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
175 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
176 </section>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
177 </inputs>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
178 <outputs>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
179 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
180 name="network_construction_report"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
181 format="pdf"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
182 label="network_construction_report.pdf"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
183 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
184 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
185 name="filtered_GEM"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
186 format="csv"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
187 label="filtered_GEM.csv">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
188 </data>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
189 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
190 name="gene_module_file"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
191 format="csv"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
192 label="gene_module_file.csv"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
193 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
194 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
195 name="network_edges_file"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
196 format="tabular"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
197 label="network_edges.txt"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
198 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
199 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
200 name="module_association_report"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
201 format="pdf"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
202 label="module_association_report.pdf">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
203 <filter>trait_data != None</filter>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
204 </data>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
205 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
206 name="gene_association_file"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
207 format="csv"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
208 label="gene_association.csv">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
209 <filter>trait_data != None</filter>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
210 </data>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
211 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
212 name="module_association_file"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
213 format="csv"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
214 label="module_association.csv">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
215 <filter>trait_data != None</filter>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
216 </data>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
217 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
218 name="updated_trait_matrix"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
219 format="csv"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
220 label="updated_trait_matrix.csv">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
221 <filter>trait_data != None</filter>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
222 </data>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
223 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
224 name="render_log_file"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
225 format="txt"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
226 label="render_log_file"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
227 hidden="false"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
228 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
229 <data
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
230 name="r_data"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
231 format="rdata"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
232 label="aurora_wgcna.RData"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
233 hidden="true"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
234 />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
235 <collection name="figures" type="list" label="Figures">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
236 <discover_datasets
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
237 pattern="__designation_and_ext__"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
238 directory="figures"
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
239 visible="false" />
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
240 </collection>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
241 </outputs>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
242 <tests>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
243 <test>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
244 <param name='expression_data' value="LiverFemale3600.gem.csv"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
245 <output name="gene_module_file" file="gene_module.csv"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
246 <output name="network_edges_file" file="network_edges.txt"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
247 <output name="network_construction_report" file="network_construction_report.html"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
248 </test>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
249 <test>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
250 <param name='expression_data' value="LiverFemale3600.gem.csv"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
251 <param name='trait_data' value="ClinicalTraits.csv"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
252 <output name="gene_module_file" file="gene_module.csv"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
253 <output name="network_edges_file" file="network_edges.txt"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
254 <output name="gene_association_file" file="gene_association_file.csv"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
255 <output name="module_association_file" file="module_association_file.csv"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
256 <output name="module_association_report" file="module_association_report.html"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
257 <output name="network_construction_report" file="network_construction_report.html"/>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
258 </test>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
259 </tests>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
260 <help><![CDATA[
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
261 This tool is a wrapper for the WGCNA R library. Please see the online
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
262 WGCNA tutorial for further details.
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
263 ]]>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
264 </help>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
265 <citations>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
266 <citation type="bibtex">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
267 @article{langfelder2008wgcna,
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
268 title={WGCNA: an R package for weighted correlation network analysis},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
269 author={Langfelder, Peter and Horvath, Steve},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
270 journal={BMC bioinformatics},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
271 volume={9},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
272 number={1},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
273 pages={559},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
274 year={2008},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
275 publisher={BioMed Central}
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
276 }
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
277 </citation>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
278 <citation type="bibtex">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
279 @article{allaire2016rmarkdown,
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
280 title={rmarkdown: Dynamic Documents for R, 2016},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
281 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
282 journal={R package version 0.9},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
283 volume={6},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
284 year={2016}
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
285 }
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
286 </citation>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
287 <citation type="bibtex">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
288 @book{xie2015dynamic,
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
289 title={Dynamic Documents with R and knitr},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
290 author={Xie, Yihui},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
291 volume={29},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
292 year={2015},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
293 publisher={CRC Press}
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
294 }
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
295 </citation>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
296 <citation type="bibtex">
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
297 @misc{dt2016,
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
298 title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
299 author = {Yihui Xie},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
300 year = {2016},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
301 note = {R package version 0.2},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
302 url = {https://CRAN.R-project.org/package=DT},
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
303 }
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
304 </citation>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
305 </citations>
c18d0db68d51 Uploaded
spficklin
parents:
diff changeset
306 </tool>