diff MetaProSIP.xml @ 5:fdb3fbfef4cc draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

--- a/MetaProSIP.xml	Thu Jan 11 17:59:18 2018 -0500
+++ b/MetaProSIP.xml	Mon Feb 12 12:54:44 2018 -0500
@@ -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.-->
+<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
 <!--Proposed Tool Section: [Utilities]-->
-<tool id="MetaProSIP" name="MetaProSIP" version="2.2.0.1">
+<tool id="MetaProSIP" name="MetaProSIP" version="2.3.0">
   <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
   <macros>
     <token name="@EXECUTABLE@">MetaProSIP</token>
@@ -10,7 +10,7 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements">
-      <requirement type="package" version="3.3.1">r-base</requirement>
+    <requirement type="package" version="3.4.1">r-base</requirement>
   </expand>
   <command>MetaProSIP
 
@@ -29,9 +29,6 @@
 #if $param_in_featureXML:
   -in_featureXML $param_in_featureXML
 #end if
-
--r_executable 'R'
-
 #if $param_mz_tolerance_ppm:
   -mz_tolerance_ppm $param_mz_tolerance_ppm
 #end if
@@ -140,7 +137,7 @@
     <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
     <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
     <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
-    <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R^2 of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
+    <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R² of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
     <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/>
     <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
       <option value="png" selected="true">png</option>
@@ -191,5 +188,5 @@
   <help>Performs proteinSIP on peptide features for elemental flux analysis.
 
 
-For more information, visit http://www.openms.de/comp/metaprosip/</help>
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaProSIP.html</help>
 </tool>