diff Analyse.xml @ 9:328f4031e5d3 draft

planemo upload commit f882a5ba78afeb368605beb3986936e86c485cbb-dirty

--- a/Analyse.xml	Wed May 10 04:12:26 2017 -0400
+++ b/Analyse.xml	Wed May 10 08:12:48 2017 -0400
@@ -1,69 +1,60 @@
 <tool id="LimmaAnalyse" name="Limma analysis" version="0.3.0">
-	<description>Perform gene expression analysis thanks to limma</description>
-	<stdio>
+
+    <description>Perform gene expression analysis thanks to limma</description>
+
+    <requirements>
+        <requirement type="package" version="0.1.0">r-smagexp</requirement>
+    </requirements>
+
+    <stdio>
         <exit_code range="1:" />
+        <regex match="Warning" source="both" level="warning"/>
     </stdio>
-	<requirements>
-	  	<!--container type="docker">sblanck/smagexp</container-->
-                <requirement type="package" version="0.1.0">r-smagexp</requirement>
-	</requirements>
-	<command>
-		<![CDATA[ 
-		Rscript
-		${__tool_directory__}/Analyse.R
-		   	--rdatainput ${rdataset}
-			--conditions ${conditions}
-		 	--selectcondition1 "${selectCondition1}"
-		    --selectcondition2 "${selectCondition2}"
-			--nbresult ${nbresult}
-       		--rdataoutput ${result_export_eset}
-       		--htmloutput $result_html 
-			--htmloutputpath $result_html.files_path
-			--tabularoutput $result_tabular
-			--htmltemplate ${__tool_directory__}/Analyse_tpl.html
-		]]>
-	</command>
-	
-	<inputs>
-		<param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
-		<param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
-		<param name="selectCondition1" type="select" label="condition 1">
-			<options from_dataset="conditions">
-    		<column name="name" index="1"/>
-    		<column name="value" index="1"/>
-    		<filter type="unique_value" column="1"/>
-		</options>
-		</param>
-		<!--param name="condition1" type="select" display="checkboxes" label="Condition 1" multiple="true">
-			<options from_dataset="conditions">
-    		<column name="name" index="2"/>
-    		<column name="value" index="0"/>
-			<filter  type="param_value" ref="selectCondition1" column="1"/>
-		</options>
-		</param-->	
-		<param name="selectCondition2" type="select" label="condition 2">
-			<options from_dataset="conditions">
-    		<column name="name" index="1"/>
-    		<column name="value" index="1"/>
-			<filter type="unique_value" column="1"/>    		
-		</options>
-		</param>	
-		<!--param name="condition2" type="select" display="checkboxes" label="Condition 2" multiple="true">
-			<options from_dataset="conditions">
-    		<column name="name" index="2"/>
-    		<column name="value" index="0"/>
-			<filter  type="param_value" ref="selectCondition2" column="1"/>
-		</options>
-		</param-->	
-		<param name="nbresult" type="integer" value="1000" min="1" label="number of top genes" help="Number of genes to be displayed in result datatable"/>
-	</inputs>
-	<outputs>
-		<data format="html" name="result_html" label="Results of analysis of ${rdataset.name}"/>
-		<data format="rdata" name="result_export_eset" label="Export of expression set of ${rdataset.name}"/>
-		<data format="tabular" name="result_tabular" label="Text Results of analysis of ${rdataset.name}"/>
-		
-	</outputs>
-	<help>
+
+    <command>
+        <![CDATA[ 
+        Rscript
+        ${__tool_directory__}/Analyse.R
+            --rdatainput ${rdataset}
+            --conditions ${conditions}
+            --selectcondition1 "${selectCondition1}"
+            --selectcondition2 "${selectCondition2}"
+            --nbresult ${nbresult}
+            --rdataoutput ${result_export_eset}
+            --htmloutput $result_html 
+            --htmloutputpath $result_html.files_path
+            --tabularoutput $result_tabular
+            --htmltemplate ${__tool_directory__}/Analyse_tpl.html
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="rdataset" type="data" format="rdata" label="RData" help="RData to be used"/>
+        <param name="conditions" type="data" format="cond" label="Conditions" help="conditions associated with the rData file"/>
+        <param name="selectCondition1" type="select" label="condition 1">
+            <options from_dataset="conditions">
+                <column name="name" index="1"/>
+                <column name="value" index="1"/>
+                <filter type="unique_value" column="1"/>
+            </options>
+        </param>
+        <param name="selectCondition2" type="select" label="condition 2">
+            <options from_dataset="conditions">
+                <column name="name" index="1"/>
+                <column name="value" index="1"/>
+                <filter type="unique_value" column="1"/>
+            </options>
+        </param>	
+        <param name="nbresult" type="integer" value="1000" min="1" label="number of top genes" help="Number of genes to be displayed in result datatable"/>
+    </inputs>
+
+    <outputs>
+        <data format="html" name="result_html" label="Results of analysis of ${rdataset.name}"/>
+        <data format="rdata" name="result_export_eset" label="Export of expression set of ${rdataset.name}"/>
+        <data format="tabular" name="result_tabular" label="Text Results of analysis of ${rdataset.name}"/>
+    </outputs>
+
+    <help>
 <![CDATA[ 
 **What it does**
 		
@@ -89,6 +80,6 @@
 - Table summarizing the differentially expressed genes and their annotations. This table is sortable and requestable.
 - Rdata object to perform further meta-analysis. 
 ]]>
-	</help>
+    </help>
 
 </tool>