# HG changeset patch
# User workflow4metabolomics
# Date 1578389387 0
# Node ID d1ec753f586f3681a112c787f957d9912e98d5c1
# Parent  144392dd4a31a87afe9d8c78b915b6c6f740d23a
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"

diff -r 144392dd4a31 -r d1ec753f586f msnbase_readmsdata.xml
--- a/msnbase_readmsdata.xml	Tue Apr 30 05:12:42 2019 -0400
+++ b/msnbase_readmsdata.xml	Tue Jan 07 09:29:47 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.1">
+<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.2">
     <description>Imports mass-spectrometry data files</description>
 
     <macros>
@@ -13,7 +13,12 @@
         @COMMAND_RSCRIPT@/msnbase_readmsdata.r
 
         #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
-            singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
+            #if $os.path.islink(str($input))
+                #set $source = $os.readlink(str($input))
+                singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)'
+            #else
+                singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
+            #end if
         #else
             zipfile '$input'
         #end if
@@ -107,7 +112,6 @@
 ‘mzData’, ‘mzXML’ and ‘mzML’.
 
 .. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
-.. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf
 
 
 -----------------
diff -r 144392dd4a31 -r d1ec753f586f repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Apr 30 05:12:42 2019 -0400
+++ b/repository_dependencies.xml	Tue Jan 07 09:29:47 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0" ?>
 <repositories>
-    <repository changeset_revision="fcc646bbf366" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="3179e95069ae" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
     <repository changeset_revision="8ce71291b600" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
 </repositories>
\ No newline at end of file