diff abims_xcms_retcor.xml @ 16:20a75ba4345b draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907

--- a/abims_xcms_retcor.xml	Mon Jan 30 08:51:40 2017 -0500
+++ b/abims_xcms_retcor.xml	Sun Feb 05 08:57:02 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.8">
+<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.1.0">
 
     <description>Retention Time Correction using retcor function from xcms R package </description>
 
@@ -33,7 +33,7 @@
             #end if
         #end if
 
-        @COMMAND_ZIPFILE_LOAD@
+        @COMMAND_FILE_LOAD@
 
         @COMMAND_LOG_EXIT@
     ]]></command>
@@ -82,7 +82,7 @@
             </when>
         </conditional>
 
-        <expand macro="zipfile_load"/>
+        <expand macro="file_load"/>
 
     </inputs>
 
@@ -133,8 +133,33 @@
             <param name="methods|options|span" value="0.2"/>
             <param name="methods|options|family" value="gaussian"/>
             <param name="methods|options|plottype" value="deviation"/>
-            <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
-            <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
+            <param name="file_load_conditional|file_load_select" value="yes" />
+            <param name="file_load_conditional|inputs|input" value="zip_file" />
+            <param name="file_load_conditional|inputs|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 4 samples" />
+                    <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
+                    <has_text text="Mass range: 200.1-600 m/z" />
+                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: KO, WT" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="image" value="faahKO-single-class.xset.group.RData"/>
+            <param name="methods|method" value="peakgroups"/>
+            <param name="methods|smooth" value="loess"/>
+            <param name="methods|extra" value="1"/>
+            <param name="methods|missing" value="1"/>
+            <param name="methods|options|option" value="show"/>
+            <param name="methods|options|span" value="0.2"/>
+            <param name="methods|options|family" value="gaussian"/>
+            <param name="methods|options|plottype" value="deviation"/>
+            <param name="file_load_conditional|file_load_select" value="yes" />
+            <param name="file_load_conditional|inputs|input" value="single_file" />
+            <param name="file_load_conditional|inputs|single_file" value="wt15.CDF,ko16.CDF,ko15.CDF,wt16.CDF"  ftype="netcdf" />
             <output name="log">
                 <assert_contents>
                     <has_text text="object with 4 samples" />
@@ -298,6 +323,10 @@
 Changelog/News
 --------------
 
+**Version 2.1.0 - 03/02/2017**
+
+- IMPROVEMENT: xcms.retcor can deal with merged individual data
+
 **Version 2.0.8 - 22/12/2016**
 
 - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph