# HG changeset patch
# User galaxyp
# Date 1508354941 14400
# Node ID 21644dec106db1659879f9e4f246bc5e4955bcb7
# Parent  a25d96e0d837e7529476e3fbdafa2892befde309
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

diff -r a25d96e0d837 -r 21644dec106d MetaProSIP.xml
--- a/MetaProSIP.xml	Wed Aug 09 09:29:30 2017 -0400
+++ b/MetaProSIP.xml	Wed Oct 18 15:29:01 2017 -0400
@@ -9,7 +9,9 @@
   </macros>
   <expand macro="references"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
+  <expand macro="requirements">
+      <requirement type="package" version="3.3.1">r-base</requirement>
+  </expand>
   <command>MetaProSIP
 
 #if $param_in_mzML:
@@ -27,9 +29,9 @@
 #if $param_in_featureXML:
   -in_featureXML $param_in_featureXML
 #end if
-#if $param_r_executable:
-  -r_executable $param_r_executable
-#end if
+
+-r_executable 'R'
+
 #if $param_mz_tolerance_ppm:
   -mz_tolerance_ppm $param_mz_tolerance_ppm
 #end if
@@ -133,7 +135,6 @@
     <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
     <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
     <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
-    <param name="param_r_executable" type="data" format="txt" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/>
     <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
     <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
     <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
diff -r a25d96e0d837 -r 21644dec106d macros.xml
--- a/macros.xml	Wed Aug 09 09:29:30 2017 -0400
+++ b/macros.xml	Wed Oct 18 15:29:01 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">
diff -r a25d96e0d837 -r 21644dec106d readme.md
--- a/readme.md	Wed Aug 09 09:29:30 2017 -0400
+++ b/readme.md	Wed Oct 18 15:29:01 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):
  
    ```
diff -r a25d96e0d837 -r 21644dec106d repository_dependencies.xml
--- a/repository_dependencies.xml	Wed Aug 09 09:29:30 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>