Mercurial > repos > bgruening > music_construct_eset

comparison construct_eset.xml @ 2:7902cd31b9b5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
author bgruening
date Sat, 29 Jan 2022 12:52:10 +0000
parents be91cb6f48e7
children 282819d09a4f
comparison
equal deleted inserted replaced
1:be91cb6f48e7 2:7902cd31b9b5
31 ## Assay Data 31 ## Assay Data
32 ## F rows of features and S columns of samples 32 ## F rows of features and S columns of samples
33 ## - This file is the only non-optional parameter 33 ## - This file is the only non-optional parameter
34 exprs_file = '$exprs_file' 34 exprs_file = '$exprs_file'
35 exprs = as.matrix(read.table(exprs_file, header = T, sep = "\t", 35 exprs = as.matrix(read.table(exprs_file, header = T, sep = "\t",
36 row.names = 1, as.is = T)) 36 row.names = 1, as.is = T, check.names=FALSE))
37 ## Phenotype Data 37 ## Phenotype Data
38 ## S rows of samples, and V columns of covariates (e.g. sex, age, etc.) 38 ## S rows of samples, and V columns of covariates (e.g. sex, age, etc.)
39 pdata = NULL 39 pdata = NULL
40 #if '$pdata_file': 40 #if '$pdata_file':
41 pdata_file = '$pdata_file' 41 pdata_file = '$pdata_file'
42 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, check.names=FALSE)
43 #end if 43 #end if
44 ## 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
45 annotation = null_str_vec('$annotation') 45 annotation = null_str_vec('$annotation')
46 if (is.null(annotation)){ 46 if (is.null(annotation)){
47 annotation = character(0) 47 annotation = character(0)
156 </repeat> 156 </repeat>
157 </section> 157 </section>
158 </inputs> 158 </inputs>
159 <outputs> 159 <outputs>
160 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: General Info" /> 160 <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: General Info" />
161 <data name="out_rds" format="rdata.eset" label="${tool.name} on ${on_string}: RData ESet Object" /> 161 <data name="out_rds" format="@RDATATYPE@" label="${tool.name} on ${on_string}: RData ESet Object" />
162 </outputs> 162 </outputs>
163 <tests> 163 <tests>
164 <test expect_num_outputs="2" >
165 <!-- Simple object -->
166 <param name="exprs_file" value="mouse_scrna_exprs.tabular" />
167 <param name="pdata_file" value="mouse_scrna_pheno.tabular" />
168 <output name="out_txt">
169 <assert_contents>
170 <has_text text="assayData: 100 features, 100 samples " />
171 </assert_contents>
172 </output>
173 </test>
164 <test expect_num_outputs="2" > 174 <test expect_num_outputs="2" >
165 <!-- Values from the manual --> 175 <!-- Values from the manual -->
166 <param name="exprs_file" value="array.tsv" /> 176 <param name="exprs_file" value="array.tsv" />
167 <param name="pdata_file" value="pheno.tsv" /> 177 <param name="pdata_file" value="pheno.tsv" />
168 <param name="annotation" value="hgu95av2" /> 178 <param name="annotation" value="hgu95av2" />