diff FileFilter.xml @ 1:2c3736b75339 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

--- a/FileFilter.xml	Wed Mar 01 10:17:49 2017 -0500
+++ b/FileFilter.xml	Tue Apr 18 15:34:13 2017 -0400
@@ -87,22 +87,42 @@
   -peak_options:remove_chromatograms
 #end if
 #if $param_peak_options_mz_precision:
-  -peak_options:mz_precision $param_peak_options_mz_precision
+  -peak_options:mz_precision
+  #if " " in str($param_peak_options_mz_precision):
+    "$param_peak_options_mz_precision"
+  #else
+    $param_peak_options_mz_precision
+  #end if
 #end if
 #if $param_peak_options_int_precision:
-  -peak_options:int_precision $param_peak_options_int_precision
+  -peak_options:int_precision
+  #if " " in str($param_peak_options_int_precision):
+    "$param_peak_options_int_precision"
+  #else
+    $param_peak_options_int_precision
+  #end if
 #end if
 #if $param_peak_options_indexed_file:
   -peak_options:indexed_file
 #end if
 #if $param_peak_options_numpress_masstime:
-  -peak_options:numpress:masstime $param_peak_options_numpress_masstime
+  -peak_options:numpress:masstime
+  #if " " in str($param_peak_options_numpress_masstime):
+    "$param_peak_options_numpress_masstime"
+  #else
+    $param_peak_options_numpress_masstime
+  #end if
 #end if
 #if $param_peak_options_numpress_masstime_error:
   -peak_options:numpress:masstime_error $param_peak_options_numpress_masstime_error
 #end if
 #if $param_peak_options_numpress_intensity:
-  -peak_options:numpress:intensity $param_peak_options_numpress_intensity
+  -peak_options:numpress:intensity
+  #if " " in str($param_peak_options_numpress_intensity):
+    "$param_peak_options_numpress_intensity"
+  #else
+    $param_peak_options_numpress_intensity
+  #end if
 #end if
 #if $param_peak_options_numpress_intensity_error:
   -peak_options:numpress:intensity_error $param_peak_options_numpress_intensity_error
@@ -183,7 +203,12 @@
   -consensus:map_and
 #end if
 #if $param_consensus_blackorwhitelist_blacklist:
-  -consensus:blackorwhitelist:blacklist $param_consensus_blackorwhitelist_blacklist
+  -consensus:blackorwhitelist:blacklist
+  #if " " in str($param_consensus_blackorwhitelist_blacklist):
+    "$param_consensus_blackorwhitelist_blacklist"
+  #else
+    $param_consensus_blackorwhitelist_blacklist
+  #end if
 #end if
 #if $param_consensus_blackorwhitelist_file:
   -consensus:blackorwhitelist:file $param_consensus_blackorwhitelist_file
@@ -281,7 +306,12 @@
   -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
 #end if
 #if $param_algorithm_SignalToNoise_write_log_messages:
-  -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages
+  -algorithm:SignalToNoise:write_log_messages
+  #if " " in str($param_algorithm_SignalToNoise_write_log_messages):
+    "$param_algorithm_SignalToNoise_write_log_messages"
+  #else
+    $param_algorithm_SignalToNoise_write_log_messages
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force: