# HG changeset patch
# User galaxyp
# Date 1503079046 14400
# Node ID d06e5c4396d7e8ea98f71e576fe2a9416f918f4f
# Parent  e6fb7acc98cce2243c8845e8ead4637f0cdb8b83
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d2b76821e22b13ed6e21795ac1b82446d8f594c6

diff -r e6fb7acc98cc -r d06e5c4396d7 MetaProSIP.xml
--- a/MetaProSIP.xml	Tue Aug 08 13:19:13 2017 -0400
+++ b/MetaProSIP.xml	Fri Aug 18 13:57:26 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 e6fb7acc98cc -r d06e5c4396d7 macros.xml
--- a/macros.xml	Tue Aug 08 13:19:13 2017 -0400
+++ b/macros.xml	Fri Aug 18 13:57:26 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">