diff MetaProSIP.xml @ 2:21644dec106d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64

--- 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) "/>