diff construct_eset.xml @ 2:7902cd31b9b5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/music/ commit 20f8561478535013e111d982b99639f48f1bea79"

--- a/construct_eset.xml	Fri Nov 26 15:55:11 2021 +0000
+++ b/construct_eset.xml	Sat Jan 29 12:52:10 2022 +0000
@@ -33,13 +33,13 @@
 ## - This file is the only non-optional parameter
 exprs_file = '$exprs_file'
 exprs = as.matrix(read.table(exprs_file, header = T, sep = "\t",
-                  row.names = 1, as.is = T))
+                  row.names = 1, as.is = T, check.names=FALSE))
 ## Phenotype Data
 ## S rows of samples, and V columns of covariates (e.g. sex, age, etc.)
 pdata = NULL
 #if '$pdata_file':
 pdata_file = '$pdata_file'
-pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T)
+pdata = read.table(pdata_file, row.names = 1, header = T, sep = "\t", as.is=T, check.names=FALSE)
 #end if
 ## Annotation and Feature Data, or just a string for type of chip used
 annotation = null_str_vec('$annotation')
@@ -158,10 +158,20 @@
     </inputs>
     <outputs>
         <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: General Info" />
-        <data name="out_rds" format="rdata.eset" label="${tool.name} on ${on_string}: RData ESet Object" />
+        <data name="out_rds" format="@RDATATYPE@" label="${tool.name} on ${on_string}: RData ESet Object" />
     </outputs>
     <tests>
         <test expect_num_outputs="2" >
+            <!-- Simple object -->
+            <param name="exprs_file" value="mouse_scrna_exprs.tabular" />
+            <param name="pdata_file" value="mouse_scrna_pheno.tabular" />
+            <output name="out_txt">
+                <assert_contents>
+                    <has_text text="assayData: 100 features, 100 samples " />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2" >
             <!-- Values from the manual -->
             <param name="exprs_file" value="array.tsv" />
             <param name="pdata_file" value="pheno.tsv" />