# HG changeset patch
# User lecorguille
# Date 1461597312 14400
# Node ID cd351af95d1482b90fc039d377c2faad566e3872
# Parent  2edfa5e1f71936af90adf6d2109bbf61788090ab
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29

diff -r 2edfa5e1f719 -r cd351af95d14 abims_xcms_fillPeaks.xml
--- a/abims_xcms_fillPeaks.xml	Fri Apr 08 10:39:59 2016 -0400
+++ b/abims_xcms_fillPeaks.xml	Mon Apr 25 11:15:12 2016 -0400
@@ -41,7 +41,7 @@
     </outputs>
     
     <tests>
-        <test>
+        <!--<test>
             <param name="image" value="xset.group.retcor.group.RData"/>
             <param name="method" value="chrom"/>
             <param name="zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
@@ -55,6 +55,21 @@
                     <has_text text="Sample classes: bio, blank" />
                 </assert_contents>
             </output>
+        </test>-->
+        <test>
+            <param name="image" value="faahKO.xset.group.retcor.group.RData"/>
+            <param name="method" value="chrom"/>
+            <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: 2506-4484 seconds (41.8-74.7 minutes)" />
+                    <has_text text="Mass range: 200.1-600 m/z" />
+                    <has_text text="Peaks: 32720 (about 8180 per sample)" />
+                    <has_text text="Peak Groups: 8157" />
+                    <has_text text="Sample classes: KO, WT" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
 
diff -r 2edfa5e1f719 -r cd351af95d14 planemo_test.sh
--- a/planemo_test.sh	Fri Apr 08 10:39:59 2016 -0400
+++ b/planemo_test.sh	Mon Apr 25 11:15:12 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_fillPeaks[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"
@@ -14,8 +13,16 @@
 #abims_xcms_fillPeaks[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_fillPeaks[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_fillpeaks/abims_xcms_fillPeaks/2.0.6[0]: passed
diff -r 2edfa5e1f719 -r cd351af95d14 test-data/faahKO.xset.group.retcor.group.RData
Binary file test-data/faahKO.xset.group.retcor.group.RData has changed
diff -r 2edfa5e1f719 -r cd351af95d14 test-data/faahKO_reduce.zip
Binary file test-data/faahKO_reduce.zip has changed
diff -r 2edfa5e1f719 -r cd351af95d14 test-data/log.txt
--- a/test-data/log.txt	Fri Apr 08 10:39:59 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-	PACKAGE INFO
-parallel	3.2.2
-BiocGenerics	0.16.1
-Biobase	2.30.0
-Rcpp	0.12.2
-mzR	2.4.1
-xcms	1.44.0
-snow	0.4.1
-batch	1.1.4
-
-
-	ARGUMENTS INFO
-xfunction	fillPeaks
-image	/tmp/tmpk97EMC/files/000/dataset_1.dat
-xsetRdataOutput	/tmp/tmpk97EMC/files/000/dataset_3.dat
-method	chrom
-zipfile	/tmp/tmpk97EMC/files/000/dataset_2.dat
-
-
-	INFILE PROCESSING INFO
-
-
-	ARGUMENTS PROCESSING INFO
-files_root_directory	 sacuri 
-Compute md5 checksum...
-
-
-	MAIN PROCESSING INFO
-sacuri/bio/HU_neg_017.mzXML 
-sacuri/bio/HU_neg_028.mzXML 
-sacuri/blank/Blanc04.mzXML 
-sacuri/blank/Blanc06.mzXML 
-
-
-null device 
-          1 
-
-
-	XSET OBJECT INFO
-An "xcmsSet" object with 4 samples
-
-Time range: 0.2-1140.1 seconds (0-19 minutes)
-Mass range: 50.0021-999.9863 m/z
-Peaks: 199718 (about 49930 per sample)
-Peak Groups: 48958 
-Sample classes: bio, blank 
-
-Profile settings: method = bin
-                  step = 0.01
-
-Memory usage: 27.3 MB
-
-
-	DONE
diff -r 2edfa5e1f719 -r cd351af95d14 test-data/sacuri_dir_root.zip
Binary file test-data/sacuri_dir_root.zip has changed
diff -r 2edfa5e1f719 -r cd351af95d14 test-data/xset.group.retcor.group.RData
Binary file test-data/xset.group.retcor.group.RData has changed