--- a/abims_xcms_group.xml	Mon Feb 22 16:31:48 2016 -0500
+++ b/abims_xcms_group.xml	Fri Apr 08 10:39:09 2016 -0400
@@ -1,20 +1,16 @@
-<tool id="abims_xcms_group" name="xcms.group" version="2.0.4">
+<tool id="abims_xcms_group" name="xcms.group" version="2.0.5">
 
     <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>
 
-    <requirements>
-        <requirement type="package" version="3.1.2">R</requirement>
-        <requirement type="binary">Rscript</requirement>
-        <requirement type="package" version="1.44.0">xcms</requirement>
-        <requirement type="package" version="2.2.0">xcms_w4m_script</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
 
-    <stdio>
-        <exit_code range="1:" level="fatal" />
-    </stdio>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
 
     <command><![CDATA[
-        xcms.r 
+        @COMMAND_XCMS_SCRIPT@
         xfunction group 
         image $image 
 
@@ -41,12 +37,7 @@
             rtCheck $methods.rtCheck
             kNN $methods.kNN
         #end if
-        ;
-        return=\$?;
-        mv log.txt $log;
-        cat $log;
-        sh -c "exit \$return"
-        
+        @COMMAND_LOG_EXIT@
    ]]></command> 
 
     <inputs>
@@ -109,41 +100,47 @@
     <tests>
         <test>
             <param name="image" value="xset.RData"/>
-            <param name="methods.method" value="density"/>
-            <param name="methods.bw" value="5"/>
-            <param name="methods.minfrac" value="0.3"/>
-            <param name="methods.mzwid" value="0.01"/>
-            <param name="methods.density_options.option" value="show"/>
-            <param name="methods.density_options.max" value="50"/>
-            <!--<output name="xsetRData" file="xset.group.RData" />-->
-            <!--<output name="rplotsPdf" file="xset.group.Rplots.pdf" />-->
+            <param name="methods|method" value="density"/>
+            <param name="methods|bw" value="5"/>
+            <param name="methods|minfrac" value="0.3"/>
+            <param name="methods|mzwid" value="0.01"/>
+            <param name="methods|density_options|option" value="show"/>
+            <param name="methods|density_options|max" value="50"/>
             <output name="log">
                 <assert_contents>
-                    <has_text text="object with 9 samples" />
-                    <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" />
-                    <has_text text="Mass range: 50.0019-999.9863 m/z" />
-                    <has_text text="Peaks: 135846 (about 15094 per sample)" />
-                    <has_text text="Peak Groups: 6642" />
+                    <has_text text="object with 4 samples" />
+                    <has_text text="Time range: 0.7-1139.7 seconds (0-19 minutes)" />
+                    <has_text text="Mass range: 50.0021-999.9863 m/z" />
+                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
+                    <has_text text="Peak Groups: 48998" />
                     <has_text text="Sample classes: bio, blank" />
                 </assert_contents>
             </output>
-         
+        </test>
+        <test>
+            <param name="image" value="xset.group.retcor.RData"/>
+            <param name="methods|method" value="density"/>
+            <param name="methods|bw" value="5"/>
+            <param name="methods|minfrac" value="0.3"/>
+            <param name="methods|mzwid" value="0.01"/>
+            <param name="methods|density_options|option" value="show"/>
+            <param name="methods|density_options|max" value="50"/>
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 4 samples" />
+                    <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
+                    <has_text text="Mass range: 50.0021-999.9863 m/z" />
+                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
+                    <has_text text="Peak Groups: 48958" />
+                    <has_text text="Sample classes: bio, blank" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
 
     <help><![CDATA[
         
-.. class:: infomark
-
-**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu 
-
-**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M]
-
- | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
-
-
-
----------------------------------------------------
+@HELP_AUTHORS@
 
 ==========
 Xcms.Group
@@ -277,6 +274,11 @@
 Changelog/News
 --------------
 
+**Version 2.0.5 - 04/04/2016**
+
+- TEST: refactoring to pass planemo test using conda dependencies 
+
+
 **Version 2.0.4 - 10/02/2016**
 
 - BUGFIX: better management of errors. Datasets remained green although the process failed
@@ -296,10 +298,7 @@
     ]]></help>
 
 
-    <citations>
-        <citation type="doi">10.1021/ac051437y</citation>
-        <citation type="doi">10.1093/bioinformatics/btu813</citation>
-    </citations>
+    <expand macro="citation" />
 
 
 </tool>