# HG changeset patch
# User galaxyp
# Date 1492544792 14400
# Node ID 580a0a6ab12fe1fe3c69d464bccf4e98c0081d44
# Parent  83818b56fd8c26172e9097b9763d984396062dcc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 83818b56fd8c -r 580a0a6ab12f OpenSwathRTNormalizer.xml
--- a/OpenSwathRTNormalizer.xml	Wed Mar 01 09:55:38 2017 -0500
+++ b/OpenSwathRTNormalizer.xml	Tue Apr 18 15:46:32 2017 -0400
@@ -65,7 +65,12 @@
   -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss:
-  -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss
+  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss):
+    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss"
+  #else
+    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss
+  #end if
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width:
   -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width
@@ -80,13 +85,23 @@
   -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages:
-  -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
+  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages):
+    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages"
+  #else
+    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages
+  #end if
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
   -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
 #end if
 #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method:
-  -algorithm:TransitionGroupPicker:PeakPickerMRM:method $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
+  -algorithm:TransitionGroupPicker:PeakPickerMRM:method
+  #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method):
+    "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method"
+  #else
+    $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method
+  #end if
 #end if
 #if $param_algorithm_DIAScoring_dia_extraction_window:
   -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window
@@ -110,7 +125,12 @@
   -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff
 #end if
 #if $param_outlierDetection_outlierMethod:
-  -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod
+  -outlierDetection:outlierMethod
+  #if " " in str($param_outlierDetection_outlierMethod):
+    "$param_outlierDetection_outlierMethod"
+  #else
+    $param_outlierDetection_outlierMethod
+  #end if
 #end if
 #if $param_outlierDetection_useIterativeChauvenet:
   -outlierDetection:useIterativeChauvenet
@@ -159,7 +179,12 @@
   -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction:
-  -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
+  -algorithm:TransitionGroupPicker:background_subtraction
+  #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction):
+    "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction"
+  #else
+    $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction
+  #end if
 #end if
     #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks:
   -algorithm:TransitionGroupPicker:recalculate_peaks     "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks"
@@ -189,34 +214,84 @@
   -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance
 #end if
     #if $adv_opts.param_algorithm_Scores_use_shape_score:
-  -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score
+  -algorithm:Scores:use_shape_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score):
+    "$adv_opts.param_algorithm_Scores_use_shape_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_shape_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_coelution_score:
-  -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score
+  -algorithm:Scores:use_coelution_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score):
+    "$adv_opts.param_algorithm_Scores_use_coelution_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_coelution_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_rt_score:
-  -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score
+  -algorithm:Scores:use_rt_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score):
+    "$adv_opts.param_algorithm_Scores_use_rt_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_rt_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_library_score:
-  -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score
+  -algorithm:Scores:use_library_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_library_score):
+    "$adv_opts.param_algorithm_Scores_use_library_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_library_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_elution_model_score:
-  -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score
+  -algorithm:Scores:use_elution_model_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score):
+    "$adv_opts.param_algorithm_Scores_use_elution_model_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_elution_model_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_intensity_score:
-  -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score
+  -algorithm:Scores:use_intensity_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score):
+    "$adv_opts.param_algorithm_Scores_use_intensity_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_intensity_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score:
-  -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score
+  -algorithm:Scores:use_nr_peaks_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score):
+    "$adv_opts.param_algorithm_Scores_use_nr_peaks_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_nr_peaks_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_total_xic_score:
-  -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score
+  -algorithm:Scores:use_total_xic_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score):
+    "$adv_opts.param_algorithm_Scores_use_total_xic_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_total_xic_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_sn_score:
-  -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score
+  -algorithm:Scores:use_sn_score
+  #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score):
+    "$adv_opts.param_algorithm_Scores_use_sn_score"
+  #else
+    $adv_opts.param_algorithm_Scores_use_sn_score
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_dia_scores:
-  -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores
+  -algorithm:Scores:use_dia_scores
+  #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores):
+    "$adv_opts.param_algorithm_Scores_use_dia_scores"
+  #else
+    $adv_opts.param_algorithm_Scores_use_dia_scores
+  #end if
 #end if
     #if $adv_opts.param_algorithm_Scores_use_ms1_correlation:
   -algorithm:Scores:use_ms1_correlation
diff -r 83818b56fd8c -r 580a0a6ab12f readme.md
--- a/readme.md	Wed Mar 01 09:55:38 2017 -0500
+++ b/readme.md	Tue Apr 18 15:46:32 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.: