# HG changeset patch
# User lecorguille
# Date 1456177744 18000
# Node ID 4ca5c7bbc6cfe2e82d8c2c86b903f3d26fd1b6da
# Parent  46e8eb12f47b5a147c25b72013fa9374a4ceb96c
planemo upload

diff -r 46e8eb12f47b -r 4ca5c7bbc6cf Makefile
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile	Mon Feb 22 16:49:04 2016 -0500
@@ -0,0 +1,23 @@
+# USAGE: make [install|clean]
+
+# -------- VARIABLE --------
+
+OBJ=camera_combinexsAnnos.tgz
+DEP=abims_CAMERA_combinexsAnnos.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 46e8eb12f47b -r 4ca5c7bbc6cf README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Feb 22 16:49:04 2016 -0500
@@ -0,0 +1,22 @@
+
+Changelog/News
+--------------
+
+**Version 2.0.3 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+
+**Version 2.0.1 - 07/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
+
+**Version 2.0.0 - 09/06/2015**
+
+- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode 
+
diff -r 46e8eb12f47b -r 4ca5c7bbc6cf abims_CAMERA_combinexsAnnos.xml
--- a/abims_CAMERA_combinexsAnnos.xml	Thu Dec 17 09:12:40 2015 -0500
+++ b/abims_CAMERA_combinexsAnnos.xml	Mon Feb 22 16:49:04 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.1">
+<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.3">
 
     <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
     
@@ -7,20 +7,24 @@
         <requirement type="binary">Rscript</requirement>
         <requirement type="package" version="1.44.0">xcms</requirement>
         <requirement type="package" version="1.22.0">camera</requirement>
-        <requirement type="package" version="2.1">camera_w4m_script</requirement>
+        <requirement type="package" version="2.2.0">camera_w4m_script</requirement>
     </requirements>
 
     <stdio>
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command>
+    <command><![CDATA[
         CAMERA.r 
-        xfunction combinexsAnnos image_pos $image_pos image_neg $image_neg
-        pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta &amp;&amp; (
-        mv variableMetadata.tsv $variableMetadata);
-        cat xset.log
-    </command>
+        xfunction combinexsAnnos 
+        image_pos $image_pos 
+        image_neg $image_neg
+
+        variableMetadataOutput $variableMetadata
+
+        pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta
+        
+    ]]></command>
 
     <inputs>
         <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
@@ -58,7 +62,7 @@
     </tests>
     
     
-    <help>
+    <help><![CDATA[
 
 .. class:: infomark
 
@@ -199,7 +203,32 @@
 
 .. image:: combinexsannos_variableMetadata.png
 
-    </help>
+
+---------------------------------------------------
+
+Changelog/News
+--------------
+
+**Version 2.0.3 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+
+**Version 2.0.1 - 07/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
+
+**Version 2.0.0 - 09/06/2015**
+
+- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode 
+
+
+    ]]></help>
 
     <citations>
         <citation type="doi"> 10.1021/ac202450g</citation>
diff -r 46e8eb12f47b -r 4ca5c7bbc6cf repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Mon Feb 22 16:49:04 2016 -0500
@@ -0,0 +1,4 @@
+<?xml version="1.0"?>
+<repositories>
+	<repository changeset_revision="4a51ab3d8ecf" name="rdata_camera_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+</repositories>
diff -r 46e8eb12f47b -r 4ca5c7bbc6cf tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Dec 17 09:12:40 2015 -0500
+++ b/tool_dependencies.xml	Mon Feb 22 16:49:04 2016 -0500
@@ -6,7 +6,7 @@
     <package name="camera" version="1.22.0">
         <repository changeset_revision="845eb883bd1b" name="package_r_camera_1_22_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="camera_w4m_script" version="2.1">
-        <repository changeset_revision="208bc3eea24c" name="package_camera_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="camera_w4m_script" version="2.2.1">
+        <repository changeset_revision="91b0d23c9d52" name="package_camera_w4m_script_2_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>