diff abims_xcms_group.xml @ 1:df264428a5e1 draft

Uploaded

--- a/abims_xcms_group.xml	Fri Aug 07 06:04:38 2015 -0400
+++ b/abims_xcms_group.xml	Mon Jan 04 08:33:29 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_group" name="xcms.group" version="2.0.2">
+<tool id="abims_xcms_group" name="xcms.group" version="2.0.4">
 
     <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>
 
@@ -13,9 +13,15 @@
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command>
+    <command><![CDATA[
         xcms.r 
-        xfunction group image $image method $methods.method sleep 0.001 
+        xfunction group 
+        image $image 
+
+        xsetRdataOutput $xsetRData
+        rplotspdf $rplotsPdf
+
+        method $methods.method sleep 0.001 
         #if $methods.method == "density":
             ## minsamp $methods.minsamp 
             minfrac $methods.minfrac 
@@ -35,12 +41,13 @@
             rtCheck $methods.rtCheck
             kNN $methods.kNN
         #end if
-        &amp;&amp; (
-        mv group.RData $xsetRData;
-        mv Rplots.pdf $rplotsPdf
-        );
-        cat xset.log
-   </command> 
+        ;
+        return=\$?;
+        mv log.txt $log;
+        cat $log;
+        sh -c "exit \$return"
+        
+   ]]></command> 
 
     <inputs>
         <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
@@ -96,6 +103,7 @@
     <outputs>
         <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
         <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
+        <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
     </outputs>
 
     <tests>
@@ -107,13 +115,23 @@
             <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" />
+            <!--<output name="xsetRData" file="xset.group.RData" />-->
+            <!--<output name="rplotsPdf" file="xset.group.Rplots.pdf" />-->
+            <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="Sample classes: bio, blank" />
+                </assert_contents>
+            </output>
          
         </test>
     </tests>
 
-    <help>
+    <help><![CDATA[
         
 .. class:: infomark
 
@@ -254,7 +272,7 @@
         :width: 700
 
 
-    </help>
+    ]]></help>
 
 
     <citations>