diff MassTraceExtractor.xml @ 1:50fc3706dbc1 draft

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

--- a/MassTraceExtractor.xml	Wed Mar 01 10:19:56 2017 -0500
+++ b/MassTraceExtractor.xml	Tue Apr 18 15:42:49 2017 -0400
@@ -39,23 +39,48 @@
   -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
 #end if
 #if $param_algorithm_mtd_reestimate_mt_sd:
-  -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd
+  -algorithm:mtd:reestimate_mt_sd
+  #if " " in str($param_algorithm_mtd_reestimate_mt_sd):
+    "$param_algorithm_mtd_reestimate_mt_sd"
+  #else
+    $param_algorithm_mtd_reestimate_mt_sd
+  #end if
 #end if
 #if $param_algorithm_mtd_quant_method:
-  -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method
+  -algorithm:mtd:quant_method
+  #if " " in str($param_algorithm_mtd_quant_method):
+    "$param_algorithm_mtd_quant_method"
+  #else
+    $param_algorithm_mtd_quant_method
+  #end if
 #end if
 #if $param_algorithm_epd_width_filtering:
-  -algorithm:epd:width_filtering $param_algorithm_epd_width_filtering
+  -algorithm:epd:width_filtering
+  #if " " in str($param_algorithm_epd_width_filtering):
+    "$param_algorithm_epd_width_filtering"
+  #else
+    $param_algorithm_epd_width_filtering
+  #end if
 #end if
 #if $param_algorithm_epd_enabled:
-  -algorithm:epd:enabled $param_algorithm_epd_enabled
+  -algorithm:epd:enabled
+  #if " " in str($param_algorithm_epd_enabled):
+    "$param_algorithm_epd_enabled"
+  #else
+    $param_algorithm_epd_enabled
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
   -force
 #end if
     #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
-  -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion
+  -algorithm:mtd:trace_termination_criterion
+  #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
+    "$adv_opts.param_algorithm_mtd_trace_termination_criterion"
+  #else
+    $adv_opts.param_algorithm_mtd_trace_termination_criterion
+  #end if
 #end if
     #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
   -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers