# HG changeset patch
# User galaxyp
# Date 1492544053 14400
# Node ID 2c3736b75339cb920caf3e3247b9e47b5f77c39f
# Parent  c0bf230a772c99f226b22c4ecc5bca2aa4e79ac8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r c0bf230a772c -r 2c3736b75339 FileFilter.xml
--- 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:
diff -r c0bf230a772c -r 2c3736b75339 readme.md
--- a/readme.md	Wed Mar 01 10:17:49 2017 -0500
+++ b/readme.md	Tue Apr 18 15:34:13 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.: