Mercurial > repos > galaxyp > openms_fidoadapter

changeset 4:935188b9c911 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:11:18 -0400
parents abd0666c9bf2
children 17e115ff19cf
files FidoAdapter.xml macros.xml readme.md repository_dependencies.xml
diffstat 4 files changed, 15 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/FidoAdapter.xml	Wed Aug 09 09:00:19 2017 -0400
+++ b/FidoAdapter.xml	Wed Oct 18 15:11:18 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
 <!--Proposed Tool Section: [ID Processing]-->
-<tool id="FidoAdapter" name="FidoAdapter" version="2.2.0">
+<tool id="FidoAdapter" name="FidoAdapter" version="2.2.0.1">
   <description>Runs the protein inference engine Fido.</description>
   <macros>
     <token name="@EXECUTABLE@">FidoAdapter</token>
@@ -11,8 +11,8 @@
   <expand macro="stdio"/>
   <expand macro="requirements"/>
   <command>FidoAdapter
--fidocp_executable fido_choose_parameters
--fido_executable fido
+-fidocp_executable FidoChooseParameters
+-fido_executable Fido
 
 #if $param_in:
   -in $param_in
--- a/macros.xml	Wed Aug 09 09:00:19 2017 -0400
+++ b/macros.xml	Wed Oct 18 15:11:18 2017 -0400
@@ -6,6 +6,7 @@
       <requirement type="package" version="15.12.15.2">xtandem</requirement>
       <requirement type="package" version="1.0">fido</requirement>
       <requirement type="package" version="2016.10.26">msgf_plus</requirement>
+      <yield/>
     </requirements>
   </xml>
   <xml name="stdio">
--- a/readme.md	Wed Aug 09 09:00:19 2017 -0400
+++ b/readme.md	Wed Oct 18 15:11:18 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):
  
    ```
--- a/repository_dependencies.xml	Wed Aug 09 09:00:19 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Required proteomics dependencies.">
-  <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
-</repositories>