# HG changeset patch
# User lecorguille
# Date 1461597291 14400
# Node ID 3b44991a8e054b8b42e2fb4e4e4822f4ce0fca7e
# Parent  54cc3edfe35ce8e5c12d0d8b5d918a723a885cd6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29

diff -r 54cc3edfe35c -r 3b44991a8e05 abims_xcms_retcor.xml
--- a/abims_xcms_retcor.xml	Fri Apr 08 10:39:32 2016 -0400
+++ b/abims_xcms_retcor.xml	Mon Apr 25 11:14:51 2016 -0400
@@ -99,7 +99,7 @@
     </outputs>
     
     <tests>
-        <test>
+        <!--<test>
             <param name="image" value="xset.group.RData"/>
             <param name="methods|method" value="peakgroups"/>
             <param name="methods|smooth" value="loess"/>
@@ -120,6 +120,28 @@
                     <has_text text="Sample classes: bio, blank" />
                 </assert_contents>
             </output>
+        </test>-->
+        <test>
+            <param name="image" value="faahKO.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="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>
     </tests>
 
diff -r 54cc3edfe35c -r 3b44991a8e05 planemo_test.sh
--- a/planemo_test.sh	Fri Apr 08 10:39:32 2016 -0400
+++ b/planemo_test.sh	Mon Apr 25 11:14:51 2016 -0400
@@ -1,11 +1,10 @@
-planemo conda_init
-planemo conda_install .
-planemo test --install_galaxy --conda_dependency_resolution --galaxy_branch "dev"
+# Example of planemo command to launch test
 
-#All 1 test(s) executed passed.
-#abims_xcms_retcor[0]: passed
+# Note: --galaxy_branch "dev" is set to deal with zip file
 
 
+# -- Use of installed package environments
+# after having installing package on a local galaxy instance
 source /w/galaxy/dev/shed_tools_tool_dependency_dir/R/3.1.2/iuc/package_r_3_1_2/1ca39eb16186/env.sh
 source /w/galaxy/dev/shed_tools_tool_dependency_dir/bioconductor-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh
 planemo test --install_galaxy --galaxy_branch "dev"
@@ -14,6 +13,16 @@
 #abims_xcms_retcor[0]: passed
 
 
+# -- Use of conda dependencies
+planemo conda_init --conda_prefix /tmp/mc
+planemo conda_install --conda_prefix /tmp/mc . 
+planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev"
+
+#All 1 test(s) executed passed.
+#abims_xcms_retcor[0]: passed
+
+
+# -- Use of shed_test
 planemo shed_test --install_galaxy --galaxy_branch "dev" -t testtoolshed
 #All 1 test(s) executed passed.
-#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/2.0.6[0]: passed
\ No newline at end of file
+#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_retcor/abims_xcms_retcor/2.0.6[0]: passed
diff -r 54cc3edfe35c -r 3b44991a8e05 test-data/faahKO.xset.group.RData
Binary file test-data/faahKO.xset.group.RData has changed
diff -r 54cc3edfe35c -r 3b44991a8e05 test-data/faahKO_reduce.zip
Binary file test-data/faahKO_reduce.zip has changed
diff -r 54cc3edfe35c -r 3b44991a8e05 test-data/sacuri_dir_root.zip
Binary file test-data/sacuri_dir_root.zip has changed
diff -r 54cc3edfe35c -r 3b44991a8e05 test-data/xset.group.RData
Binary file test-data/xset.group.RData has changed