# HG changeset patch
# User galaxyp
# Date 1492544818 14400
# Node ID 34479f097d1b0a1b6caf81032ed8b03d031d2e8e
# Parent  99766e79672126ce5e2a005227bf553c1ad12efc
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 99766e796721 -r 34479f097d1b OpenSwathWorkflow.xml
--- a/OpenSwathWorkflow.xml	Wed Mar 01 10:17:37 2017 -0500
+++ b/OpenSwathWorkflow.xml	Tue Apr 18 15:46:58 2017 -0400
@@ -67,7 +67,12 @@
   -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width
 #end if
 #if $param_Scoring_TransitionGroupPicker_background_subtraction:
-  -Scoring:TransitionGroupPicker:background_subtraction $param_Scoring_TransitionGroupPicker_background_subtraction
+  -Scoring:TransitionGroupPicker:background_subtraction
+  #if " " in str($param_Scoring_TransitionGroupPicker_background_subtraction):
+    "$param_Scoring_TransitionGroupPicker_background_subtraction"
+  #else
+    $param_Scoring_TransitionGroupPicker_background_subtraction
+  #end if
 #end if
 #if $param_Scoring_TransitionGroupPicker_recalculate_peaks:
   -Scoring:TransitionGroupPicker:recalculate_peaks     "$param_Scoring_TransitionGroupPicker_recalculate_peaks"
@@ -103,10 +108,20 @@
   -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages
 #end if
 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks:
-  -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks
+  #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks):
+    "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks"
+  #else
+    $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks
+  #end if
 #end if
 #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method:
-  -Scoring:TransitionGroupPicker:PeakPickerMRM:method $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
+  -Scoring:TransitionGroupPicker:PeakPickerMRM:method
+  #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method):
+    "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method"
+  #else
+    $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method
+  #end if
 #end if
 #if $param_Scoring_DIAScoring_dia_extraction_window:
   -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window
@@ -133,7 +148,12 @@
   -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration
 #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
@@ -200,16 +220,31 @@
   -use_elution_model_score
 #end if
     #if $adv_opts.param_readOptions:
-  -readOptions $adv_opts.param_readOptions
+  -readOptions
+  #if " " in str($adv_opts.param_readOptions):
+    "$adv_opts.param_readOptions"
+  #else
+    $adv_opts.param_readOptions
+  #end if
 #end if
     #if $adv_opts.param_mz_correction_function:
-  -mz_correction_function $adv_opts.param_mz_correction_function
+  -mz_correction_function
+  #if " " in str($adv_opts.param_mz_correction_function):
+    "$adv_opts.param_mz_correction_function"
+  #else
+    $adv_opts.param_mz_correction_function
+  #end if
 #end if
     #if $adv_opts.param_tempDirectory:
   -tempDirectory     "$adv_opts.param_tempDirectory"
 #end if
     #if $adv_opts.param_extraction_function:
-  -extraction_function $adv_opts.param_extraction_function
+  -extraction_function
+  #if " " in str($adv_opts.param_extraction_function):
+    "$adv_opts.param_extraction_function"
+  #else
+    $adv_opts.param_extraction_function
+  #end if
 #end if
     #if $adv_opts.param_batchSize:
   -batchSize $adv_opts.param_batchSize
@@ -224,31 +259,76 @@
   -Scoring:write_convex_hull
 #end if
     #if $adv_opts.param_Scoring_Scores_use_shape_score:
-  -Scoring:Scores:use_shape_score $adv_opts.param_Scoring_Scores_use_shape_score
+  -Scoring:Scores:use_shape_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score):
+    "$adv_opts.param_Scoring_Scores_use_shape_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_shape_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_coelution_score:
-  -Scoring:Scores:use_coelution_score $adv_opts.param_Scoring_Scores_use_coelution_score
+  -Scoring:Scores:use_coelution_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_coelution_score):
+    "$adv_opts.param_Scoring_Scores_use_coelution_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_coelution_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_rt_score:
-  -Scoring:Scores:use_rt_score $adv_opts.param_Scoring_Scores_use_rt_score
+  -Scoring:Scores:use_rt_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_rt_score):
+    "$adv_opts.param_Scoring_Scores_use_rt_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_rt_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_library_score:
-  -Scoring:Scores:use_library_score $adv_opts.param_Scoring_Scores_use_library_score
+  -Scoring:Scores:use_library_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_library_score):
+    "$adv_opts.param_Scoring_Scores_use_library_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_library_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_intensity_score:
-  -Scoring:Scores:use_intensity_score $adv_opts.param_Scoring_Scores_use_intensity_score
+  -Scoring:Scores:use_intensity_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_intensity_score):
+    "$adv_opts.param_Scoring_Scores_use_intensity_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_intensity_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score:
-  -Scoring:Scores:use_nr_peaks_score $adv_opts.param_Scoring_Scores_use_nr_peaks_score
+  -Scoring:Scores:use_nr_peaks_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_nr_peaks_score):
+    "$adv_opts.param_Scoring_Scores_use_nr_peaks_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_nr_peaks_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_total_xic_score:
-  -Scoring:Scores:use_total_xic_score $adv_opts.param_Scoring_Scores_use_total_xic_score
+  -Scoring:Scores:use_total_xic_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_total_xic_score):
+    "$adv_opts.param_Scoring_Scores_use_total_xic_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_total_xic_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_sn_score:
-  -Scoring:Scores:use_sn_score $adv_opts.param_Scoring_Scores_use_sn_score
+  -Scoring:Scores:use_sn_score
+  #if " " in str($adv_opts.param_Scoring_Scores_use_sn_score):
+    "$adv_opts.param_Scoring_Scores_use_sn_score"
+  #else
+    $adv_opts.param_Scoring_Scores_use_sn_score
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_dia_scores:
-  -Scoring:Scores:use_dia_scores $adv_opts.param_Scoring_Scores_use_dia_scores
+  -Scoring:Scores:use_dia_scores
+  #if " " in str($adv_opts.param_Scoring_Scores_use_dia_scores):
+    "$adv_opts.param_Scoring_Scores_use_dia_scores"
+  #else
+    $adv_opts.param_Scoring_Scores_use_dia_scores
+  #end if
 #end if
     #if $adv_opts.param_Scoring_Scores_use_ms1_correlation:
   -Scoring:Scores:use_ms1_correlation
diff -r 99766e796721 -r 34479f097d1b readme.md
--- a/readme.md	Wed Mar 01 10:17:37 2017 -0500
+++ b/readme.md	Tue Apr 18 15:46:58 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.: