diff readme.md @ 2:73585e6601d8 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

--- a/readme.md	Wed Aug 09 09:12:37 2017 -0400
+++ b/readme.md	Wed Oct 18 15:18:53 2017 -0400
@@ -69,6 +69,7 @@
      omssa_executable pepnovo_executable \
      xtandem_executable param_model_directory \
      java_executable java_memory java_permgen \
+     r_executable rt_concat_trafo_out \
     -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \
     -s PATH/TO/SKIP_TOOLS_FILES.txt
     ```
@@ -77,8 +78,8 @@
  * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example:
 
     ```
-    sed -i '13 a\-fido_executable fido' wrappers/FidoAdapter.xml
-    sed -i '13 a\-fidocp_executable fido_choose_parameters' wrappers/FidoAdapter.xml
+    sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml
+    sed -i '13 a\-fidocp_executable FidoChooseParameters' wrappers/FidoAdapter.xml
     sed -i '13 a\-myrimatch_executable myrimatch' wrappers/MyriMatchAdapter.xml
     sed -i '13 a\-omssa_executable omssa' wrappers/OMSSAAdapter.xml
     sed -i '13 a\-xtandem_executable xtandem' wrappers/XTandemAdapter.xml
@@ -117,6 +118,14 @@
     ]]>
     ```
     
+ * In `MetaProSIP.xml` add `R` as a requirement:
+ 
+   ```
+   <expand macro="requirements">
+       <requirement type="package" version="3.3.1">r-base</requirement>
+   </expand>
+   ```
+   
  * In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
  
    ```