# HG changeset patch
# User lecorguille
# Date 1467636395 14400
# Node ID 465623d2f6fa17f742631cd4ad9afb9922eb8eb6
# Parent  cd351af95d1482b90fc039d377c2faad566e3872
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82

diff -r cd351af95d14 -r 465623d2f6fa abims_xcms_fillPeaks.xml
--- a/abims_xcms_fillPeaks.xml	Mon Apr 25 11:15:12 2016 -0400
+++ b/abims_xcms_fillPeaks.xml	Mon Jul 04 08:46:35 2016 -0400
@@ -18,9 +18,8 @@
 
         method $method
 
-        #if $zip_file:
-            zipfile $zip_file
-        #end if
+        @COMMAND_ZIPFILE_LOAD@
+
         @COMMAND_LOG_EXIT@ 
         
     ]]></command>
@@ -31,8 +30,9 @@
             <option value="chrom" selected="true">chrom</option>
             <option value="MSW" >MSW</option>
         </param>
-        <!-- To pass planemo test -->
-        <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." />
+        
+        <expand macro="zipfile_load"/>
+
     </inputs>
 
     <outputs>
@@ -59,7 +59,8 @@
         <test>
             <param name="image" value="faahKO.xset.group.retcor.group.RData"/>
             <param name="method" value="chrom"/>
-            <param name="zip_file" value="faahKO_reduce.zip"  ftype="zip" />
+            <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
+            <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip"  ftype="zip" />
             <output name="log">
                 <assert_contents>
                     <has_text text="object with 4 samples" />
diff -r cd351af95d14 -r 465623d2f6fa macros.xml
--- a/macros.xml	Mon Apr 25 11:15:12 2016 -0400
+++ b/macros.xml	Mon Jul 04 08:46:35 2016 -0400
@@ -3,9 +3,9 @@
     <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>
+            <requirement type="package" version="0.4_1">r-snow</requirement>
+            <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
+            <requirement type="package" version="1.1_4">r-batch</requirement>
         </requirements>
     </xml>
     <xml name="stdio">
@@ -26,6 +26,30 @@
         sh -c "exit \$return"
     </token>
 
+    <!-- zipfile load for planemo test -->
+
+    <token name="@COMMAND_ZIPFILE_LOAD@">
+        #if $zipfile_load_conditional.zip_file:
+            zipfile $zipfile_load_conditional.zip_file
+        #end if
+    </token>
+
+    <xml name="zipfile_load">
+        <conditional name="zipfile_load_conditional">
+            <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." >
+                <option value="no" >no need</option>
+                <option value="yes" selected="peakgroups">yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">
+                <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" />
+            </when>
+        </conditional>
+    </xml>
+
+
+
     <token name="@HELP_AUTHORS@">
 .. class:: infomark
 
diff -r cd351af95d14 -r 465623d2f6fa planemo_test.sh
--- a/planemo_test.sh	Mon Apr 25 11:15:12 2016 -0400
+++ b/planemo_test.sh	Mon Jul 04 08:46:35 2016 -0400
@@ -1,13 +1,11 @@
 # Example of planemo command to launch test
 
-# Note: --galaxy_branch "dev" is set to deal with zip file
-
 
 # -- Use of installed package environments
 # after having installing package on a local galaxy instance
 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-xcms/1.44.0/lecorguille/package_bioconductor_xcms_1_44_0/0c38f7d43e08/env.sh
-planemo test --install_galaxy --galaxy_branch "dev"
+planemo test --install_galaxy
 
 #All 1 test(s) executed passed.
 #abims_xcms_fillPeaks[0]: passed
@@ -16,7 +14,7 @@
 # -- Use of conda dependencies
 planemo conda_init --conda_prefix /tmp/mc
 planemo conda_install --conda_prefix /tmp/mc . 
-planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution --galaxy_branch "dev"
+planemo test --install_galaxy --conda_prefix /tmp/mc --conda_dependency_resolution
 
 #All 1 test(s) executed passed.
 #abims_xcms_fillPeaks[0]: passed
diff -r cd351af95d14 -r 465623d2f6fa tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Apr 25 11:15:12 2016 -0400
+++ b/tool_dependencies.xml	Mon Jul 04 08:46:35 2016 -0400
@@ -3,7 +3,7 @@
     <package name="R" version="3.1.2">
         <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="bioconductor-xcms" version="1.44.0">
-        <repository changeset_revision="58ebb405a3d6" name="package_bioconductor_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="bioconductor-xcms" version="1.46.0">
+        <repository changeset_revision="779207ed5674" name="package_bioconductor_xcms_1_46_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>