Mercurial > repos > galaxyp > openms_spectramerger

diff SpectraMerger.xml @ 1:4726f1062f33 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 15:55:34 -0400
parents c561e6fb46d8
children 84ba2c7e5d9b
line wrap: on
line diff
--- a/SpectraMerger.xml	Wed Mar 01 10:11:40 2017 -0500
+++ b/SpectraMerger.xml	Tue Apr 18 15:55:34 2017 -0400
@@ -19,10 +19,20 @@
   -out $param_out
 #end if
 #if $param_merging_method:
-  -merging_method $param_merging_method
+  -merging_method
+  #if " " in str($param_merging_method):
+    "$param_merging_method"
+  #else
+    $param_merging_method
+  #end if
 #end if
 #if $param_algorithm_average_gaussian_spectrum_type:
-  -algorithm:average_gaussian:spectrum_type $param_algorithm_average_gaussian_spectrum_type
+  -algorithm:average_gaussian:spectrum_type
+  #if " " in str($param_algorithm_average_gaussian_spectrum_type):
+    "$param_algorithm_average_gaussian_spectrum_type"
+  #else
+    $param_algorithm_average_gaussian_spectrum_type
+  #end if
 #end if
 #if $param_algorithm_average_gaussian_ms_level:
   -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level
@@ -31,7 +41,12 @@
   -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM
 #end if
 #if $param_algorithm_average_tophat_spectrum_type:
-  -algorithm:average_tophat:spectrum_type $param_algorithm_average_tophat_spectrum_type
+  -algorithm:average_tophat:spectrum_type
+  #if " " in str($param_algorithm_average_tophat_spectrum_type):
+    "$param_algorithm_average_tophat_spectrum_type"
+  #else
+    $param_algorithm_average_tophat_spectrum_type
+  #end if
 #end if
 #if $param_algorithm_average_tophat_ms_level:
   -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level
@@ -40,7 +55,12 @@
   -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range
 #end if
 #if $param_algorithm_average_tophat_rt_unit:
-  -algorithm:average_tophat:rt_unit $param_algorithm_average_tophat_rt_unit
+  -algorithm:average_tophat:rt_unit
+  #if " " in str($param_algorithm_average_tophat_rt_unit):
+    "$param_algorithm_average_tophat_rt_unit"
+  #else
+    $param_algorithm_average_tophat_rt_unit
+  #end if
 #end if
 
 #if $rep_param_algorithm_block_method_ms_levels:
@@ -73,10 +93,20 @@
   -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width
 #end if
     #if $adv_opts.param_algorithm_mz_binning_width_unit:
-  -algorithm:mz_binning_width_unit $adv_opts.param_algorithm_mz_binning_width_unit
+  -algorithm:mz_binning_width_unit
+  #if " " in str($adv_opts.param_algorithm_mz_binning_width_unit):
+    "$adv_opts.param_algorithm_mz_binning_width_unit"
+  #else
+    $adv_opts.param_algorithm_mz_binning_width_unit
+  #end if
 #end if
     #if $adv_opts.param_algorithm_sort_blocks:
-  -algorithm:sort_blocks $adv_opts.param_algorithm_sort_blocks
+  -algorithm:sort_blocks
+  #if " " in str($adv_opts.param_algorithm_sort_blocks):
+    "$adv_opts.param_algorithm_sort_blocks"
+  #else
+    $adv_opts.param_algorithm_sort_blocks
+  #end if
 #end if
     #if $adv_opts.param_algorithm_average_gaussian_cutoff:
   -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff