Mercurial > repos > bgruening > music_construct_eset

comparison construct_eset.xml @ 1:be91cb6f48e7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 683bb72ae92b5759a239b7e3bf4c5a229ed35b54"
author bgruening
date Fri, 26 Nov 2021 15:55:11 +0000
parents 2cfd0db49bbc
children 7902cd31b9b5
comparison
equal deleted inserted replaced
0:2cfd0db49bbc 1:be91cb6f48e7
12 <configfile name="conf" > 12 <configfile name="conf" >
13 13
14 suppressWarnings(suppressPackageStartupMessages(library(xbioc))) 14 suppressWarnings(suppressPackageStartupMessages(library(xbioc)))
15 suppressWarnings(suppressPackageStartupMessages(library(MuSiC))) 15 suppressWarnings(suppressPackageStartupMessages(library(MuSiC)))
16 16
17 null_str_vec = function(gstr){ 17 null_str_vec = function(gstr, is.str=FALSE){
18 tokens = unlist(as.vector(strsplit(gstr, split=","))) 18 tokens = unlist(as.vector(strsplit(gstr, split=",")))
19 if (length(tokens) == 0){ 19 if (length(tokens) == 0){
20 if (is.str){
21 return(character(0))
22 }
20 return(NULL) 23 return(NULL)
21 } 24 }
22 if (length(tokens) == 1){ 25 if (length(tokens) == 1){
23 return(tokens[[1]]) 26 return(tokens[[1]])
24 } 27 }
38 pdata_file = '$pdata_file' 41 pdata_file = '$pdata_file'
39 pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T) 42 pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T)
40 #end if 43 #end if
41 ## Annotation and Feature Data, or just a string for type of chip used 44 ## Annotation and Feature Data, or just a string for type of chip used
42 annotation = null_str_vec('$annotation') 45 annotation = null_str_vec('$annotation')
46 if (is.null(annotation)){
47 annotation = character(0)
48 }
43 49
44 if (all(rownames(pdata) != colnames(exprs))) { 50 if (all(rownames(pdata) != colnames(exprs))) {
45 stop("Number of Samples between phenotypes and assays are not the same") 51 stop("Number of Samples between phenotypes and assays are not the same")
46 } 52 }
47 53
64 rownames(metadata) = unlist(metadata\$lname) 70 rownames(metadata) = unlist(metadata\$lname)
65 metadata\$ldesc = NULL 71 metadata\$ldesc = NULL
66 metadata\$lname = NULL 72 metadata\$lname = NULL
67 73
68 if (nrow(metadata)==0) { 74 if (nrow(metadata)==0) {
69 metadata = NULL 75 pheno_data = new("AnnotatedDataFrame", data = pdata)
70 } 76 } else {
71 77 pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata)
72 pheno_data = new("AnnotatedDataFrame", data = pdata, varMetadata = metadata) 78 }
79
73 80
74 ## Experiment Description -- using the MIAME object 81 ## Experiment Description -- using the MIAME object
75 experiment_data = new( 82 experiment_data = new(
76 "MIAME", 83 "MIAME",
77 name = null_str_vec('$expdata.name'), 84 name = null_str_vec('$expdata.name', is.str=T),
78 lab = null_str_vec('$expdata.lab'), 85 lab = null_str_vec('$expdata.lab', is.str=T),
79 contact = null_str_vec('$expdata.contact'), 86 contact = null_str_vec('$expdata.contact', is.str=T),
80 title = null_str_vec('$expdata.title'), 87 title = null_str_vec('$expdata.title', is.str=T),
81 abstract = null_str_vec('$expdata.abstract'), 88 abstract = null_str_vec('$expdata.abstract', is.str=T),
82 url = null_str_vec('$expdata.url'), 89 url = null_str_vec('$expdata.url', is.str=T),
83 other = list( 90 other = list(
84 #for i, row in enumerate($expdata.other): 91 #for i, row in enumerate($expdata.other):
85 #if i==0 92 #if i==0
86 '$row.field' = null_str_vec('$row.comment') 93 '$row.field' = null_str_vec('$row.comment', is.str=T)
87 #else 94 #else
88 ,'$row.field' = null_str_vec('$row.comment') 95 ,'$row.field' = null_str_vec('$row.comment', is.str=T)
89 #end if 96 #end if
90 #end for 97 #end for
91 )) 98 ))
92 99
93 e_set = ExpressionSet(assayData = exprs, 100 e_set = ExpressionSet(assayData = exprs,
94 phenoData = pheno_data, 101 phenoData = pheno_data,
95 experimentData = experiment_data, 102 experimentData = experiment_data,
96 annotation = annotation) 103 annotation = annotation)
97 104
98 capture.output(print(e_set), file = '$out_tab') 105 capture.output(print(e_set), file = '$out_txt')
99 saveRDS(e_set, file= '$out_rds') 106 saveRDS(e_set, file= '$out_rds')
100 107
101 </configfile> 108 </configfile>
102 </configfiles> 109 </configfiles>
103 <inputs> 110 <inputs>
110 optional="true" help="A string detailing which chip was used" > 117 optional="true" help="A string detailing which chip was used" >
111 <expand macro="validator_text_and_urls" /> 118 <expand macro="validator_text_and_urls" />
112 </param> 119 </param>
113 <repeat name="metadata" title="Meta Data" min="0" max="15" > 120 <repeat name="metadata" title="Meta Data" min="0" max="15" >
114 <!-- optional, so min=0 --> 121 <!-- optional, so min=0 -->
115 <param name="row_names" label="Label" type="text" > 122 <param name="row_names" label="Label" type="text"
123 help="Metadata should correspond directly to the columns of the Phenotype Data" >
116 <expand macro="validator_text_and_urls" /> 124 <expand macro="validator_text_and_urls" />
117 </param> 125 </param>
118 <param name="label_desc" label="Label Description" type="text" > 126 <param name="label_desc" label="Label Description" type="text" >
119 <expand macro="validator_text_and_urls" /> 127 <expand macro="validator_text_and_urls" />
120 </param> 128 </param>
147 </param> 155 </param>
148 </repeat> 156 </repeat>
149 </section> 157 </section>
150 </inputs> 158 </inputs>
151 <outputs> 159 <outputs>
152 <data name="out_tab" format="tabular" label="${tool.name} on ${on_string}: General Info" /> 160 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: General Info" />
153 <data name="out_rds" format="rdata.eset" label="${tool.name} on ${on_string}: RData ESet Object" /> 161 <data name="out_rds" format="rdata.eset" label="${tool.name} on ${on_string}: RData ESet Object" />
154 </outputs> 162 </outputs>
155 <tests> 163 <tests>
156 <test expect_num_outputs="2" > 164 <test expect_num_outputs="2" >
157 <!-- Values from the manual --> 165 <!-- Values from the manual -->
184 <repeat name="other" > 192 <repeat name="other" >
185 <param name="field" value="general" /> 193 <param name="field" value="general" />
186 <param name="comment" value="Some other comment" /> 194 <param name="comment" value="Some other comment" />
187 </repeat> 195 </repeat>
188 </section> 196 </section>
189 <output name="out_tab"> 197 <output name="out_txt">
190 <assert_contents> 198 <assert_contents>
191 <has_text text="assayData: 3 features, 2 samples " /> 199 <has_text text="assayData: 3 features, 2 samples " />
192 </assert_contents> 200 </assert_contents>
193 </output> 201 </output>
194 </test> 202 </test>