# HG changeset patch
# User lecorguille
# Date 1460126412 14400
# Node ID ca7c9a6da2c6eca9eea9bf9e1ad342493c42c067
# Parent  df7b3b846cb6b794735a032155fd75b7d834bde7
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6

diff -r df7b3b846cb6 -r ca7c9a6da2c6 README.rst
--- a/README.rst	Fri Mar 18 10:44:23 2016 -0400
+++ b/README.rst	Fri Apr 08 10:40:12 2016 -0400
@@ -2,7 +2,22 @@
 Changelog/News
 --------------
 
+**Version 1.0.1 - 04/04/2016**
+
+- TEST: refactoring to pass planemo test using conda dependencies
+
+
 **Version 1.0.0 - 10/02/2016**
 
 - NEW: Create a summary of XCMS analysis
 
+
+Test Status
+-----------
+
+Planemo test using conda: failed
+
+Planemo test using source env.sh: passed
+
+Planemo shed_test : passed
+
diff -r df7b3b846cb6 -r ca7c9a6da2c6 abims_xcms_summary.xml
--- a/abims_xcms_summary.xml	Fri Mar 18 10:44:23 2016 -0400
+++ b/abims_xcms_summary.xml	Fri Apr 08 10:40:12 2016 -0400
@@ -1,20 +1,21 @@
-<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.0">
+<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.1">
     
     <description>Create a summary of XCMS analysis</description>
-    
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>    
+
     <requirements>
         <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="1.22.0">camera</requirement>
+        <requirement type="package" version="1.22.0">bioconductor-camera</requirement>
+        <requirement type="package" version="1.1_4">r-batch</requirement>
     </requirements>
     
-    <stdio>
-        <exit_code range="1:" level="fatal" />
-    </stdio>
+    <expand macro="stdio"/>
     
-    <command interpreter="Rscript"><![CDATA[
-        xcms_summary.r
+    <command><![CDATA[
+        $__tool_directory__/xcms_summary.r
 
         image $image 
         htmlOutput $htmlOutput
@@ -35,19 +36,13 @@
     <tests>
         <test>
             <param name="image" value="fillpeaks.RData" />
-            <output name="htmlOutput" file="summary.html" ftype="html" />
+            <output name="htmlOutput" file="summary.html" />
         </test>
     </tests>
     
     <help><![CDATA[
-
-.. class:: infomark
-
-**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff part of Workflow4Metabolomics.org [W4M]
-
- | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
-
----------------------------------------------------
+        
+@HELP_AUTHORS@
 
 ============
 Xcms.summary
@@ -65,6 +60,11 @@
 Changelog/News
 --------------
 
+**Version 1.0.1 - 04/04/2016**
+
+- TEST: refactoring to pass planemo test using conda dependencies
+
+
 **Version 1.0.0 - 10/02/2016**
 
 - NEW: Create a summary of XCMS analysis
@@ -73,8 +73,6 @@
     ]]></help>
 
 
-    <citations>
-        <citation type="doi">10.1093/bioinformatics/btu813</citation>
-    </citations>
+    <expand macro="citation" />
 
 </tool>
diff -r df7b3b846cb6 -r ca7c9a6da2c6 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Apr 08 10:40:12 2016 -0400
@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="3.1.2">R</requirement>
+	    <requirement type="package" version="0.4_1">r-snow</requirement>
+            <requirement type="package" version="1.44.0">bioconductor-xcms</requirement>
+	    <requirement type="package" version="1.1_4">r-batch</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1" level="fatal" />
+        </stdio>
+    </xml>
+
+    <token name="@COMMAND_XCMS_SCRIPT@">
+        LANG=C Rscript $__tool_directory__/xcms.r
+    </token>
+
+    <token name="@COMMAND_LOG_EXIT@">
+        ;
+        return=\$?;
+        mv log.txt $log;
+        cat $log;
+        sh -c "exit \$return"
+    </token>
+
+    <token name="@HELP_AUTHORS@">
+.. class:: infomark
+
+**Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu 
+
+.. class:: infomark
+
+**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
+
+ | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
+
+---------------------------------------------------
+
+    </token>
+
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1021/ac051437y</citation>
+            <citation type="doi">10.1093/bioinformatics/btu813</citation>
+        </citations>
+    </xml>
+</macros>
diff -r df7b3b846cb6 -r ca7c9a6da2c6 planemo.sh
--- a/planemo.sh	Fri Mar 18 10:44:23 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-planemo shed_init -f --name=xcms_summary --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS analysis" --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\nThis tool create a HTML summary of XCMS analysis" --category="Metabolomics"
diff -r df7b3b846cb6 -r ca7c9a6da2c6 planemo_test.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo_test.sh	Fri Apr 08 10:40:12 2016 -0400
@@ -0,0 +1,21 @@
+planemo conda_init
+planemo conda_install .
+#Linking packages ...
+#Error: ERROR: placeholder '/root/miniconda3/envs/_build_placehold_placehold_placehold_placehold_placehold_p' too short in: ncurses-5.9-4
+
+
+
+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-camera/1.22.0/lecorguille/package_bioconductor_camera_1_22_0/22cec61d66c2/env.sh
+planemo test --install_galaxy
+
+#All 1 test(s) executed passed.
+#abims_xcms_summary[0]: passed
+
+
+planemo shed_test --install_galaxy --galaxy_branch "dev" 
+
+#All 2 test(s) executed passed.
+#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.0.8[0]: passed
+#testtoolshed.g2.bx.psu.edu/repos/lecorguille/xcms_xcmsset/abims_xcms_xcmsSet/2.0.8[1]: passed
+
diff -r df7b3b846cb6 -r ca7c9a6da2c6 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Mar 18 10:44:23 2016 -0400
+++ b/tool_dependencies.xml	Fri Apr 08 10:40:12 2016 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="camera" version="1.22.0">
+    <package name="bioconductor-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>
 </tool_dependency>
diff -r df7b3b846cb6 -r ca7c9a6da2c6 xcms_summary.r
--- a/xcms_summary.r	Fri Mar 18 10:44:23 2016 -0400
+++ b/xcms_summary.r	Fri Apr 08 10:40:12 2016 -0400
@@ -1,5 +1,5 @@
-#!/usr/local/public/bin/Rscript --vanilla --slave --no-site-file
-# version="0.1.0"
+#!/usr/bin/env Rscript
+# version="1.0.0"
 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABIMS TEAM