diff FeatureFinderMultiplex.xml @ 3:477b8f9a8c18 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit daf6dfc513ede9b890125d9fff2c2657d834eea9

--- a/FeatureFinderMultiplex.xml	Thu Apr 27 12:49:34 2017 -0400
+++ b/FeatureFinderMultiplex.xml	Fri Jul 14 18:45:00 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: [Quantitation]-->
-<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.1.0">
+<tool id="FeatureFinderMultiplex" name="FeatureFinderMultiplex" version="2.2.0">
   <description>Determination of peak ratios in LC-MS data</description>
   <macros>
     <token name="@EXECUTABLE@">FeatureFinderMultiplex</token>
@@ -72,6 +72,14 @@
     #if $adv_opts.param_algorithm_knock_out:
   -algorithm:knock_out
 #end if
+    #if $adv_opts.param_algorithm_spectrum_type:
+  -algorithm:spectrum_type
+  #if " " in str($adv_opts.param_algorithm_spectrum_type):
+    "$adv_opts.param_algorithm_spectrum_type"
+  #else
+    $adv_opts.param_algorithm_spectrum_type
+  #end if
+#end if
     #if $adv_opts.param_algorithm_averagine_type:
   -algorithm:averagine_type
   #if " " in str($adv_opts.param_algorithm_averagine_type):
@@ -165,6 +173,11 @@
       </param>
       <param name="param_algorithm_averagine_similarity_scaling" type="float" min="0.0" max="1.0" optional="True" value="0.75" label="Let x denote this scaling factor, and p the averagine similarity paramete" help="(-averagine_similarity_scaling) For the detection of single peptides, the averagine parameter p is replaced by p' = p + x(1-p), i.e. x = 0 -&gt; p' = p and x = 1 -&gt; p' = 1. (For knock_out = true, peptide doublets and singlets are detected simulataneously. For singlets, the peptide similarity filter is irreleavant. In order to compensate for this 'missing filter', the averagine parameter p is replaced by the more restrictive p' when searching for singlets.)"/>
       <param name="param_algorithm_knock_out" display="radio" type="boolean" truevalue="-algorithm:knock_out" falsevalue="" checked="false" optional="True" label="Is it likely that knock-outs are present?" help="(-knock_out) (Supported for doublex, triplex and quadruplex experiments only.)"/>
+      <param name="param_algorithm_spectrum_type" display="radio" type="select" optional="False" value="automatic" label="Type of MS1 spectra in input mzML file" help="(-spectrum_type) 'automatic' determines the spectrum type directly from the input mzML file">
+        <option value="profile">profile</option>
+        <option value="centroid">centroid</option>
+        <option value="automatic" selected="true">automatic</option>
+      </param>
       <param name="param_algorithm_averagine_type" display="radio" type="select" optional="False" value="peptide" label="The type of averagine to use, currently RNA, DNA or peptide" help="(-averagine_type) ">
         <option value="peptide" selected="true">peptide</option>
         <option value="RNA">RNA</option>