# HG changeset patch
# User galaxyp
# Date 1508336602 14400
# Node ID 90a1fdfa03723dd671b2974db7e5e8ad113912de
# Parent ea6647067793cb323d221167fe2361e89d2bd839
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 26556c08813e892b4d1eed0e98012601870cae5f
diff -r ea6647067793 -r 90a1fdfa0372 readme.md
--- a/readme.md Fri Aug 18 14:16:06 2017 -0400
+++ b/readme.md Wed Oct 18 10:23:22 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:
+
+ ```
+
+ r-base
+
+ ```
+
* In `IDFileConverter.xml` the following is needed in the command section at the beginning (check your file to know what to copy where):
```
diff -r ea6647067793 -r 90a1fdfa0372 repository_dependencies.xml
--- a/repository_dependencies.xml Fri Aug 18 14:16:06 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-
-
-
-