Mercurial > repos > bgruening > music_construct_eset
comparison construct_eset.xml @ 2:7902cd31b9b5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"
author | bgruening |
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date | Sat, 29 Jan 2022 12:52:10 +0000 |
parents | be91cb6f48e7 |
children | 282819d09a4f |
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1:be91cb6f48e7 | 2:7902cd31b9b5 |
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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" /> |