Mercurial > repos > marie-tremblay-metatoul > nmr_normalization

changeset 1:fc66c35dcd4f draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/nmr_normalization commit 1634b22a58db1c33119dda35ffa3127d2e1b7928
author lecorguille
date Mon, 04 Jul 2016 11:53:19 -0400
parents e1b29d705286
children
files NmrNormalization_xml.xml
diffstat 1 files changed, 21 insertions(+), 21 deletions(-) [+]
line wrap: on
line diff
--- a/NmrNormalization_xml.xml	Mon Apr 18 11:29:30 2016 -0400
+++ b/NmrNormalization_xml.xml	Mon Jul 04 11:53:19 2016 -0400
@@ -2,16 +2,16 @@
     
     <description>Normalization of NMR bucketed and integrated spectra</description>
 
-    <requirements>
-        <requirement type="package" version="3.1.2">R</requirement>
-	      <requirement type="package" version="1.1_4">r-batch</requirement>
+    <requirements>
+        <requirement type="package" version="3.1.2">R</requirement>
+	      <requirement type="package" version="1.1_4">r-batch</requirement>
     </requirements>
     
-	  <stdio>
-        <exit_code range="1:" level="fatal" />
-    </stdio>
-
-    <command>
+	  <stdio>
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+
+    <command>
         Rscript $__tool_directory__/NmrNormalization_wrapper.R
 
 		    ## Data matrix of bucketed and integrated spectra
@@ -84,23 +84,23 @@
     
 	<outputs>
 		<data format="txt" name="logOut" label="${tool.name}_log" />
-		<data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" />
 		<data format="tabular" name="sampleMetadataOut" label="${tool.name}_samplemetadata" />
 		<data format="tabular" name="variableMetadataOut" label="${tool.name}_variableMetadataOut" />
+        <data format="tabular" name="dataMatrixOut" label="${tool.name}_bucketedData" />
 		<data format="pdf" name="graphOut" label="${tool.name}_spectra" >
 			<filter> graphType != "None" </filter>
 		</data>
 	</outputs>
   
-  <tests>
-        <test>
-            <param name="dataMatrix" value="MTBLS1_bucketedData.tabular" ftype="tabular" />
-            <param name="scalingMethod|method" value="Total" />
-            <param name="graphType" value="Overlay" />
-            <output name="dataMatrixOut" file="MTBLS1_bucketedData_normalized.tabular" />
-            <output name="sampleMetadataOut" file="MTBLS1_sampleMetadata_normalized.tabular" />
-            <output name="variableMetadataOut" file="MTBLS1_variableMetadata_normalized.tabular" />
-        </test>
+  <tests>
+        <test>
+            <param name="dataMatrix" value="MTBLS1_bucketedData.tabular" ftype="tabular" />
+            <param name="scalingMethod|method" value="Total" />
+            <param name="graphType" value="Overlay" />
+            <output name="dataMatrixOut" file="MTBLS1_bucketedData_normalized.tabular" />
+            <output name="sampleMetadataOut" file="MTBLS1_sampleMetadata_normalized.tabular" />
+            <output name="variableMetadataOut" file="MTBLS1_variableMetadata_normalized.tabular" />
+        </test>
     </tests>
 
 	<help>
@@ -255,9 +255,9 @@
         :width: 100
 
 
-   </help>
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/btu813</citation>
+   </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu813</citation>
     </citations>
 </tool>