diff isa2w4m.xml @ 1:1facef3ba64a draft default tip

"planemo upload commit 9683b1655539660ed1e983783a72a5c3016238bd-dirty"

--- a/isa2w4m.xml	Wed Jan 08 09:56:00 2020 -0500
+++ b/isa2w4m.xml	Wed Apr 27 16:38:56 2022 +0000
@@ -1,10 +1,11 @@
 <!-- vi: se fdm=marker : -->
-<tool id="isa2w4m" name="ISA to W4M" version="1.1.1">
+<tool id="isa2w4m" name="ISA to W4M" version="1.1.3">
 
 	<description>Convert ISA data type into W4M format</description>
 
 	<requirements>
-		<requirement type="package" version="0.10.3">isatools</requirement>
+		<requirement type="package" version="1.2.5">pandas</requirement>
+		<requirement type="package" version="0.12.2">isatools</requirement>
 	</requirements>
 
 	<!-- Command {{{1 -->
@@ -13,29 +14,33 @@
 		## @@@BEGIN_CHEETAH@@@
 
 		$__tool_directory__/isa2w4m.py
-		-i "$isa.extra_files_path"
-		-s "$w4m_sample_metadata"
-		-v "$w4m_variable_metadata"
-		-m "$w4m_data_matrix"
+		-i '$isa.extra_files_path'
+		-s '$w4m_sample_metadata'
+		-v '$w4m_variable_metadata'
+		-m '$w4m_data_matrix'
 
 		## Choose study to output
 		#if $study:
-			-n "$study"
+			-n '$study'
 		#end if
 
 		## Choose assay to output
 		#if $assay:
-			-f "$assay"
+			-f '$assay'
 		#end if
 
 		## Filtering
 		#if $sample_na_filtering:
-			-S "$sample_na_filtering"
+			-S '$sample_na_filtering'
 		#end if
 		#if $variable_na_filtering:
-			-V "$variable_na_filtering"
+			-V '$variable_na_filtering'
 		#end if
 
+		## Redirect stderr to stdout otherwise Galaxy thinks the tool fails if
+		## it sees just one character on stderr.
+		2>&1
+
 		## @@@END_CHEETAH@@@
 	]]></command>
 
@@ -65,6 +70,12 @@
 			<output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/>
 			<output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/>
 		</test>
+		<test>
+			<param name="isa" value="MTBLS174.zip" ftype="isa-tab"/>
+			<output name="w4m_variable_metadata" file="MTBLS174-w4m-variable-metadata.tsv"/>
+			<output name="w4m_sample_metadata" file="MTBLS174-w4m-sample-metadata.tsv"/>
+			<output name="w4m_data_matrix" file="MTBLS174-w4m-sample-variable-matrix.tsv"/>
+		</test>
 	</tests>
 
 	<!-- Help {{{1 -->