# HG changeset patch
# User lecorguille
# Date 1456176708 18000
# Node ID 98e33cdf0eb112f909c4714e54a5892a3217b152
# Parent  ed149026836eac37b855c9eb3225ecde9fe3694d
planemo upload

diff -r ed149026836e -r 98e33cdf0eb1 Makefile
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile	Mon Feb 22 16:31:48 2016 -0500
@@ -0,0 +1,23 @@
+# USAGE: make [install|clean]
+
+# -------- VARIABLE --------
+
+OBJ=xcms_group.tgz
+DEP=abims_xcms_group.xml tool_dependencies.xml repository_dependencies.xml static test-data
+
+
+# ------------------------
+
+all: $(OBJ)
+
+$(OBJ): $(DEP)
+	tar --exclude=".svn" -zchf $@ $^
+
+# ------------------------
+
+install: $(OBJ)
+	mv *.tgz ~
+
+clean:
+	rm *.tgz
+
diff -r ed149026836e -r 98e33cdf0eb1 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Feb 22 16:31:48 2016 -0500
@@ -0,0 +1,19 @@
+
+Changelog/News
+--------------
+
+**Version 2.0.4 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+- UPDATE: refactoring to feed the new report tool
+
+
+**Version 2.0.2 - 02/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
diff -r ed149026836e -r 98e33cdf0eb1 abims_xcms_group.xml
--- a/abims_xcms_group.xml	Tue Nov 24 06:23:44 2015 -0500
+++ b/abims_xcms_group.xml	Mon Feb 22 16:31:48 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>
 
@@ -6,16 +6,22 @@
         <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="2.1">xcms_w4m_script</requirement>
+        <requirement type="package" version="2.2.0">xcms_w4m_script</requirement>
     </requirements>
 
     <stdio>
         <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
 
@@ -254,8 +272,28 @@
         :width: 700
 
 
+---------------------------------------------------
 
-    </help>
+Changelog/News
+--------------
+
+**Version 2.0.4 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+- UPDATE: refactoring to feed the new report tool
+
+
+**Version 2.0.2 - 02/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
+
+    ]]></help>
 
 
     <citations>
diff -r ed149026836e -r 98e33cdf0eb1 planemo.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo.sh	Mon Feb 22 16:31:48 2016 -0500
@@ -0,0 +1,1 @@
+planemo shed_init -f --name=xcms_group --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Group peaks from different samples together" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nGroup peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics"
diff -r ed149026836e -r 98e33cdf0eb1 test-data/log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log.txt	Mon Feb 22 16:31:48 2016 -0500
@@ -0,0 +1,51 @@
+	PACKAGE INFO
+parallel	3.1.2
+BiocGenerics	0.14.0
+Biobase	2.28.0
+Rcpp	0.12.0
+mzR	2.2.2
+xcms	1.44.0
+snow	0.3.13
+batch	1.1.4
+
+
+	ARGUMENTS INFO
+xfunction	group
+image	test-data/xset.RData
+xsetRdataOutput	test-data/xset.group.RData
+rplotspdf	xset.group.Rplots.pdf
+method	density
+sleep	0.001
+minfrac	0.5
+bw	30
+mzwid	0.25
+
+
+	INFILE PROCESSING INFO
+
+
+	ARGUMENTS PROCESSING INFO
+
+
+	MAIN PROCESSING INFO
+112 175 237 300 362 425 487 550 612 675 737 800 862 925 987 
+null device 
+          1 
+
+
+	XSET OBJECT INFO
+An "xcmsSet" object with 9 samples
+
+Time range: 0.7-1140 seconds (0-19 minutes)
+Mass range: 50.0019-999.9863 m/z
+Peaks: 135846 (about 15094 per sample)
+Peak Groups: 6642 
+Sample classes: bio, blank 
+
+Profile settings: method = bin
+                  step = 0.01
+
+Memory usage: 15 MB
+
+
+	DONE
diff -r ed149026836e -r 98e33cdf0eb1 test-data/xset.group.RData
Binary file test-data/xset.group.RData has changed
diff -r ed149026836e -r 98e33cdf0eb1 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Nov 24 06:23:44 2015 -0500
+++ b/tool_dependencies.xml	Mon Feb 22 16:31:48 2016 -0500
@@ -6,7 +6,7 @@
     <package name="xcms" version="1.44.0">
         <repository changeset_revision="4443617bdd85" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="xcms_w4m_script" version="2.1">
-        <repository changeset_revision="c94c8ef520c8" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="xcms_w4m_script" version="2.2.0">
+        <repository changeset_revision="115cf2b43a3c" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>