# HG changeset patch
# User galaxyp
# Date 1625784335 0
# Node ID e42225f8a659c71895958097fcf89fada0186427
# Parent  181bd6a5f6ce937ca46acbe172ba45423d658006
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9ee3c66acde2e5690b93eca561db78b58df2a07d"

diff -r 181bd6a5f6ce -r e42225f8a659 macros.xml
--- a/macros.xml	Fri Jun 25 07:18:03 2021 +0000
+++ b/macros.xml	Thu Jul 08 22:45:35 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0" ?>
 <macros>
     <token name="@VERSION@">1.6.17.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@VERSION_PTXQC@">1.0.10</token>
     <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token>
     <token name="@TMT2PLEX@">
diff -r 181bd6a5f6ce -r e42225f8a659 maxquant.xml
--- a/maxquant.xml	Fri Jun 25 07:18:03 2021 +0000
+++ b/maxquant.xml	Thu Jul 08 22:45:35 2021 +0000
@@ -32,7 +32,11 @@
     #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
     #for $target, $link in zip($infiles, $names_with_ext)
         &&
+        #if str($input_opts.ftype) == '.thermo.raw':
+        cp '$target' '$link'
+        #else:
         ln -s '$target' '$link'
+        #end if
     #end for
     &&
     python3 '$__tool_directory__/create_mqpar.py'
@@ -454,7 +458,6 @@
                 <option value="4">Unspecific</option>
                 <option value="5">No digestion</option>
             </param>
-
             <conditional name="quant_method">
                 <param name="select_quant_method" type="select" label="Quantitation Methods"
                        help="Select a method if needed.">