# HG changeset patch
# User galaxyp
# Date 1492545886 14400
# Node ID 15cc4acac8c35ae7fade441b6ba83cfad60f5e5d
# Parent  2602a6da5ad3604173970f8ddfb4537b63b17b0e
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 2602a6da5ad3 -r 15cc4acac8c3 FeatureFinderMetabo.xml
--- a/FeatureFinderMetabo.xml	Wed Mar 01 12:21:06 2017 -0500
+++ b/FeatureFinderMetabo.xml	Tue Apr 18 16:04:46 2017 -0400
@@ -31,16 +31,36 @@
   -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm
 #end if
 #if $param_algorithm_mtd_reestimate_mt_sd:
-  -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd
+  -algorithm:mtd:reestimate_mt_sd
+  #if " " in str($param_algorithm_mtd_reestimate_mt_sd):
+    "$param_algorithm_mtd_reestimate_mt_sd"
+  #else
+    $param_algorithm_mtd_reestimate_mt_sd
+  #end if
 #end if
 #if $param_algorithm_mtd_quant_method:
-  -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method
+  -algorithm:mtd:quant_method
+  #if " " in str($param_algorithm_mtd_quant_method):
+    "$param_algorithm_mtd_quant_method"
+  #else
+    $param_algorithm_mtd_quant_method
+  #end if
 #end if
 #if $param_algorithm_epd_enabled:
-  -algorithm:epd:enabled $param_algorithm_epd_enabled
+  -algorithm:epd:enabled
+  #if " " in str($param_algorithm_epd_enabled):
+    "$param_algorithm_epd_enabled"
+  #else
+    $param_algorithm_epd_enabled
+  #end if
 #end if
 #if $param_algorithm_epd_width_filtering:
-  -algorithm:epd:width_filtering $param_algorithm_epd_width_filtering
+  -algorithm:epd:width_filtering
+  #if " " in str($param_algorithm_epd_width_filtering):
+    "$param_algorithm_epd_width_filtering"
+  #else
+    $param_algorithm_epd_width_filtering
+  #end if
 #end if
 #if $param_algorithm_ffm_charge_lower_bound:
   -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound
@@ -49,10 +69,20 @@
   -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound
 #end if
 #if $param_algorithm_ffm_enable_RT_filtering:
-  -algorithm:ffm:enable_RT_filtering $param_algorithm_ffm_enable_RT_filtering
+  -algorithm:ffm:enable_RT_filtering
+  #if " " in str($param_algorithm_ffm_enable_RT_filtering):
+    "$param_algorithm_ffm_enable_RT_filtering"
+  #else
+    $param_algorithm_ffm_enable_RT_filtering
+  #end if
 #end if
 #if $param_algorithm_ffm_isotope_filtering_model:
-  -algorithm:ffm:isotope_filtering_model $param_algorithm_ffm_isotope_filtering_model
+  -algorithm:ffm:isotope_filtering_model
+  #if " " in str($param_algorithm_ffm_isotope_filtering_model):
+    "$param_algorithm_ffm_isotope_filtering_model"
+  #else
+    $param_algorithm_ffm_isotope_filtering_model
+  #end if
 #end if
 #if $param_algorithm_ffm_mz_scoring_13C:
   -algorithm:ffm:mz_scoring_13C
@@ -65,7 +95,12 @@
   -force
 #end if
     #if $adv_opts.param_algorithm_mtd_trace_termination_criterion:
-  -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion
+  -algorithm:mtd:trace_termination_criterion
+  #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion):
+    "$adv_opts.param_algorithm_mtd_trace_termination_criterion"
+  #else
+    $adv_opts.param_algorithm_mtd_trace_termination_criterion
+  #end if
 #end if
     #if $adv_opts.param_algorithm_mtd_trace_termination_outliers:
   -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers
@@ -98,7 +133,12 @@
   -algorithm:ffm:report_summed_ints
 #end if
     #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities:
-  -algorithm:ffm:use_smoothed_intensities $adv_opts.param_algorithm_ffm_use_smoothed_intensities
+  -algorithm:ffm:use_smoothed_intensities
+  #if " " in str($adv_opts.param_algorithm_ffm_use_smoothed_intensities):
+    "$adv_opts.param_algorithm_ffm_use_smoothed_intensities"
+  #else
+    $adv_opts.param_algorithm_ffm_use_smoothed_intensities
+  #end if
 #end if
 #end if
 </command>
diff -r 2602a6da5ad3 -r 15cc4acac8c3 readme.md
--- a/readme.md	Wed Mar 01 12:21:06 2017 -0500
+++ b/readme.md	Tue Apr 18 16:04:46 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.: