# HG changeset patch
# User galaxyp
# Date 1492544346 14400
# Node ID ef60d14798078f397b7ecc6c0f6e0b3a5bbcbd67
# Parent  fd36e0bbb6a289b648d6c5f2441b1cc1445ebd02
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r fd36e0bbb6a2 -r ef60d1479807 IsobaricAnalyzer.xml
--- a/IsobaricAnalyzer.xml	Sat Apr 08 08:30:24 2017 -0400
+++ b/IsobaricAnalyzer.xml	Tue Apr 18 15:39:06 2017 -0400
@@ -13,7 +13,12 @@
   <command>IsobaricAnalyzer
 
 #if $param_type:
-  -type $param_type
+  -type
+  #if " " in str($param_type):
+    "$param_type"
+  #else
+    $param_type
+  #end if
 #end if
 #if $param_in:
   -in $param_in
@@ -25,7 +30,12 @@
   -id_pool     "$param_id_pool"
 #end if
 #if $param_extraction_select_activation:
-  -extraction:select_activation '$param_extraction_select_activation'
+  -extraction:select_activation
+  #if " " in str($param_extraction_select_activation):
+    "$param_extraction_select_activation"
+  #else
+    $param_extraction_select_activation
+  #end if
 #end if
 #if $param_extraction_reporter_mass_shift:
   -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift
@@ -34,7 +44,12 @@
   -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity
 #end if
 #if $param_extraction_keep_unannotated_precursor:
-  -extraction:keep_unannotated_precursor $param_extraction_keep_unannotated_precursor
+  -extraction:keep_unannotated_precursor
+  #if " " in str($param_extraction_keep_unannotated_precursor):
+    "$param_extraction_keep_unannotated_precursor"
+  #else
+    $param_extraction_keep_unannotated_precursor
+  #end if
 #end if
 #if $param_extraction_min_reporter_intensity:
   -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity
@@ -110,7 +125,12 @@
   #end for
 #end if
 #if $param_quantification_isotope_correction:
-  -quantification:isotope_correction $param_quantification_isotope_correction
+  -quantification:isotope_correction
+  #if " " in str($param_quantification_isotope_correction):
+    "$param_quantification_isotope_correction"
+  #else
+    $param_quantification_isotope_correction
+  #end if
 #end if
 #if $param_quantification_normalization:
   -quantification:normalization
@@ -146,7 +166,12 @@
   -tmt10plex:channel_131_description     "$param_tmt10plex_channel_131_description"
 #end if
 #if $param_tmt10plex_reference_channel:
-  -tmt10plex:reference_channel $param_tmt10plex_reference_channel
+  -tmt10plex:reference_channel
+  #if " " in str($param_tmt10plex_reference_channel):
+    "$param_tmt10plex_reference_channel"
+  #else
+    $param_tmt10plex_reference_channel
+  #end if
 #end if
 
 #if $rep_param_tmt10plex_correction_matrix:
@@ -199,7 +224,12 @@
   -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation
 #end if
     #if $adv_opts.param_extraction_purity_interpolation:
-  -extraction:purity_interpolation $adv_opts.param_extraction_purity_interpolation
+  -extraction:purity_interpolation
+  #if " " in str($adv_opts.param_extraction_purity_interpolation):
+    "$adv_opts.param_extraction_purity_interpolation"
+  #else
+    $adv_opts.param_extraction_purity_interpolation
+  #end if
 #end if
 #end if
 </command>
diff -r fd36e0bbb6a2 -r ef60d1479807 readme.md
--- a/readme.md	Sat Apr 08 08:30:24 2017 -0400
+++ b/readme.md	Tue Apr 18 15:39:06 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.: