changeset 3:003373d58672 draft

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Makefile	Mon Feb 22 17:03:29 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
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Feb 22 17:03:29 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.
+

--- a/abims_xcms_group.xml	Mon Jan 04 10:39:46 2016 -0500
+++ b/abims_xcms_group.xml	Mon Feb 22 17:03:29 2016 -0500
@@ -272,6 +272,27 @@
         :width: 700
 
 
+---------------------------------------------------
+
+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>
 
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo.sh	Mon Feb 22 17:03:29 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"

--- a/tool_dependencies.xml	Mon Jan 04 10:39:46 2016 -0500
+++ b/tool_dependencies.xml	Mon Feb 22 17:03:29 2016 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="73cd1d529330" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="xcms" version="1.44.0">
         <repository changeset_revision="8ea252413ed6" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="xcms_w4m_script" version="2.2.0">
-        <repository changeset_revision="e0d3e1caf5d9" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f54521c7a50c" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>