# HG changeset patch
# User lecorguille
# Date 1511966719 18000
# Node ID c934dd5c49a9fe8e7ef49802fbc6a0127d88dab0
# Parent  15646e937936fb715ce32531c11f797cf304e645
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 4897a06ef248e2e74e57a496dd68adbda3c828f1

diff -r 15646e937936 -r c934dd5c49a9 README.rst
--- a/README.rst	Fri Apr 07 07:35:01 2017 -0400
+++ b/README.rst	Wed Nov 29 09:45:19 2017 -0500
@@ -13,15 +13,19 @@
 
 **How**
 
- - The file `destinations_input_type.py` (shiped with this tool) must be place in `lib/galaxy/jobs/rules/`
- - The `job_conf.xml` must be inspired by the `job_conf.xml.sample` shiped with this tool
- - The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py`
- - Restart Galaxy
+1. The file [`destinations_input_type.py`](https://raw.githubusercontent.com/workflow4metabolomics/xcms/master/galaxy/xcms_xcmsset/destinations_input_type.py) (shiped with this tool) must be place in `lib/galaxy/jobs/rules/`
+2. The `job_conf.xml` must be inspired by the [`job_conf.xml.sample`](https://github.com/workflow4metabolomics/xcms/blob/master/galaxy/xcms_xcmsset/job_conf.xml.sample) shiped with this tool
+3. The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py`
+4. Restart Galaxy
 
 
 Changelog/News
 --------------
 
+**Version 2.1.1 - 29/11/2017**
+
+- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
+
 **Version 2.1.0 - 22/02/2017**
 
 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
diff -r 15646e937936 -r c934dd5c49a9 abims_xcms_xcmsSet.xml
--- a/abims_xcms_xcmsSet.xml	Fri Apr 07 07:35:01 2017 -0400
+++ b/abims_xcms_xcmsSet.xml	Wed Nov 29 09:45:19 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.0">
+<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.1.1">
     <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
 
     <macros>
@@ -557,6 +557,10 @@
 Changelog/News
 --------------
 
+**Version 2.1.1 - 29/11/2017**
+
+- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
+
 **Version 2.1.0 - 22/02/2017**
 
 - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group".
@@ -593,7 +597,7 @@
 - TEST: refactoring to feed the new report tool
 
 
-**Version 2.0.2 - 18/01/2016
+**Version 2.0.2 - 18/01/2016**
 
 - BUGFIX: Some zip files were tag as "corrupt" by R. We have changed the extraction mode to deal with thoses cases.
 
diff -r 15646e937936 -r c934dd5c49a9 destinations_input_type.py
--- a/destinations_input_type.py	Fri Apr 07 07:35:01 2017 -0400
+++ b/destinations_input_type.py	Wed Nov 29 09:45:19 2017 -0500
@@ -18,6 +18,6 @@
     input_extension = inp_data[ "input" ].extension
     log.debug("The input extension is %s" % input_extension)
     if input_extension in ["mzxml","mzml","mzdata","netcdf"]:
-        return 'thread1-men_free10'
+        return 'thread1-mem_free10'
     else: # zip file
         return 'thread4-men_free10'
diff -r 15646e937936 -r c934dd5c49a9 job_conf.xml.sample
--- a/job_conf.xml.sample	Fri Apr 07 07:35:01 2017 -0400
+++ b/job_conf.xml.sample	Wed Nov 29 09:45:19 2017 -0500
@@ -2,7 +2,6 @@
 <!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
 <job_conf>
     <plugins>
-        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
         <plugin id="sge" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" type="runner"/>
         <plugin id="dynamic" type="runner" >
             <param id="rules_module">galaxy.jobs.rules</param>
@@ -12,11 +11,10 @@
         <handler id="main"/>
     </handlers>
     <destinations default="sge_default">
-        <destination id="local" runner="local"/>
         <destination id="sge_default" runner="sge">
              <param id="nativeSpecification">-V -w n -q galaxy.q</param>
         </destination>
-        
+
         <destination id="thread1-men_free10" runner="sge">
              <param id="nativeSpecification">-V -w n -q galaxy.q -pe thread 1 -R y -l mem_free=10G </param>
         </destination>
@@ -31,6 +29,5 @@
     </destinations>
     <tools>
         <tool destination="python_destination_input_type" id="abims_xcms_xcmsSet" />
-        <tool destination="local" id="upload1"/>
     </tools>
 </job_conf>
diff -r 15646e937936 -r c934dd5c49a9 macros.xml
--- a/macros.xml	Fri Apr 07 07:35:01 2017 -0400
+++ b/macros.xml	Wed Nov 29 09:45:19 2017 -0500
@@ -19,7 +19,7 @@
     </xml>
 
     <token name="@COMMAND_XCMS_SCRIPT@">
-        LANG=C Rscript $__tool_directory__/xcms.r
+        LC_ALL=C Rscript $__tool_directory__/xcms.r
     </token>
 
     <token name="@COMMAND_LOG_EXIT@">