# HG changeset patch
# User galaxyp
# Date 1492544451 14400
# Node ID 06987761999d0bcb59b940f2eaf7651167452cdc
# Parent  65a1b411e9327137f0976d71f2c97ddce1eaa185
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 65a1b411e932 -r 06987761999d MSGFPlusAdapter.xml
--- a/MSGFPlusAdapter.xml	Wed Mar 01 10:17:13 2017 -0500
+++ b/MSGFPlusAdapter.xml	Tue Apr 18 15:40:51 2017 -0400
@@ -12,29 +12,29 @@
   <expand macro="requirements"/>
   <command><![CDATA[
 
-## check input file type
-#set $in_type = $param_in.ext
+ ## check input file type
+ #set $in_type = $param_in.ext
 
-## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files
-ln -s '$param_in' 'param_in.${in_type}' &&
-ln -s '$param_database' param_database.fasta &&
-## find location of the MSGFPlus.jar file of the msgf_plus conda package
-MSGF_JAR=\$(msgf_plus -get_jar_path) &&
+ ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files
+ ln -s '$param_in' 'param_in.${in_type}' &&
+ ln -s '$param_database' param_database.fasta &&
+ ## find location of the MSGFPlus.jar file of the msgf_plus conda package
+ MSGF_JAR=\$(msgf_plus -get_jar_path) &&
 
-MSGFPlusAdapter
--executable \$MSGF_JAR
-#if $param_in:
-  -in 'param_in.${in_type}'
-#end if
-#if $param_out:
-  -out $param_out
-#end if
-#if $param_mzid_out:
-  -mzid_out $param_mzid_out
-#end if
-#if $param_database:
-  -database param_database.fasta
-#end if
+ MSGFPlusAdapter
+ -executable \$MSGF_JAR
+ #if $param_in:
+   -in 'param_in.${in_type}'
+ #end if
+ #if $param_out:
+   -out $param_out
+ #end if
+ #if $param_mzid_out:
+   -mzid_out $param_mzid_out
+ #end if
+ #if $param_database:
+   -database param_database.fasta
+ #end if
 #if $param_add_decoys:
   -add_decoys
 #end if
@@ -42,25 +42,55 @@
   -precursor_mass_tolerance $param_precursor_mass_tolerance
 #end if
 #if $param_precursor_error_units:
-  -precursor_error_units $param_precursor_error_units
+  -precursor_error_units
+  #if " " in str($param_precursor_error_units):
+    "$param_precursor_error_units"
+  #else
+    $param_precursor_error_units
+  #end if
 #end if
 #if $param_isotope_error_range:
   -isotope_error_range     "$param_isotope_error_range"
 #end if
 #if $param_fragment_method:
-  -fragment_method $param_fragment_method
+  -fragment_method
+  #if " " in str($param_fragment_method):
+    "$param_fragment_method"
+  #else
+    $param_fragment_method
+  #end if
 #end if
 #if $param_instrument:
-  -instrument $param_instrument
+  -instrument
+  #if " " in str($param_instrument):
+    "$param_instrument"
+  #else
+    $param_instrument
+  #end if
 #end if
 #if $param_enzyme:
-  -enzyme $param_enzyme
+  -enzyme
+  #if " " in str($param_enzyme):
+    "$param_enzyme"
+  #else
+    $param_enzyme
+  #end if
 #end if
 #if $param_protocol:
-  -protocol $param_protocol
+  -protocol
+  #if " " in str($param_protocol):
+    "$param_protocol"
+  #else
+    $param_protocol
+  #end if
 #end if
 #if $param_tryptic:
-  -tryptic $param_tryptic
+  -tryptic
+  #if " " in str($param_tryptic):
+    "$param_tryptic"
+  #else
+    $param_tryptic
+  #end if
 #end if
 #if $param_min_precursor_charge:
   -min_precursor_charge $param_min_precursor_charge
@@ -113,7 +143,7 @@
   -force
 #end if
 #end if
-]]>
+ ]]>
 </command>
   <inputs>
     <param name="param_in" type="data" format="mzxml,mgf,mzml" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
diff -r 65a1b411e932 -r 06987761999d readme.md
--- a/readme.md	Wed Mar 01 10:17:13 2017 -0500
+++ b/readme.md	Tue Apr 18 15:40:51 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.: