# HG changeset patch
# User galaxyp
# Date 1508354553 14400
# Node ID 22e9bb7d151afe03ccb89fce2a25770977c74bc4
# Parent cd0746ee47969429e8927a5ec778d1cccc407211
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
diff -r cd0746ee4796 -r 22e9bb7d151a XTandemAdapter.xml
--- a/XTandemAdapter.xml Wed Aug 09 09:18:43 2017 -0400
+++ b/XTandemAdapter.xml Wed Oct 18 15:22:33 2017 -0400
@@ -132,7 +132,7 @@
-
+
diff -r cd0746ee4796 -r 22e9bb7d151a macros.xml
--- a/macros.xml Wed Aug 09 09:18:43 2017 -0400
+++ b/macros.xml Wed Oct 18 15:22:33 2017 -0400
@@ -6,6 +6,7 @@
xtandem
fido
msgf_plus
+
diff -r cd0746ee4796 -r 22e9bb7d151a readme.md
--- a/readme.md Wed Aug 09 09:18:43 2017 -0400
+++ b/readme.md Wed Oct 18 15:22:33 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 cd0746ee4796 -r 22e9bb7d151a repository_dependencies.xml
--- a/repository_dependencies.xml Wed Aug 09 09:18:43 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-
-
-
-