# HG changeset patch
# User galaxyp
# Date 1492545334 14400
# Node ID 4726f1062f33e1819683f4b33c4527840594d20e
# Parent  c561e6fb46d8f21a9733ca73394744158ba2dc7a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r c561e6fb46d8 -r 4726f1062f33 SpectraMerger.xml
--- 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
diff -r c561e6fb46d8 -r 4726f1062f33 readme.md
--- a/readme.md	Wed Mar 01 10:11:40 2017 -0500
+++ b/readme.md	Tue Apr 18 15:55:34 2017 -0400
@@ -39,10 +39,10 @@
  * clone or install CTD2Galaxy
 
     ```bash
-    git clone https://github.com/blankclemens/CTD2Galaxy.git
+    git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
     ```
     
- * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. 
+ * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository.
 
     ```bash
     python generator.py \ 
@@ -102,13 +102,6 @@
     [...]
     ]]>
     ```
- * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line
- 
-        -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
-     
-   and change it to
-   
-        -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
 
  * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: