diff ConsensusID.xml @ 3:9d7e3e5da94a draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

--- a/ConsensusID.xml	Thu Apr 27 13:16:39 2017 -0400
+++ b/ConsensusID.xml	Wed Aug 09 09:30:14 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: [ID Processing]-->
-<tool id="ConsensusID" name="ConsensusID" version="2.1.0">
+<tool id="ConsensusID" name="ConsensusID" version="2.2.0">
   <description>Computes a consensus of peptide identifications of several identification engines.</description>
   <macros>
     <token name="@EXECUTABLE@">ConsensusID</token>
@@ -65,7 +65,7 @@
 #end if
 </command>
   <inputs>
-    <param name="param_in" type="data" format="featurexml,consensusxml,idxml" optional="False" label="input file" help="(-in) "/>
+    <param name="param_in" type="data" format="idxml,featurexml,consensusxml" optional="False" label="input file" help="(-in) "/>
     <param name="param_rt_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed retention time deviation between identifications belonging to the same spectrum" help="(-rt_delta) "/>
     <param name="param_mz_delta" type="float" min="0.0" optional="True" value="0.1" label="[idXML input only] Maximum allowed precursor m/z deviation between identifications belonging to the same spectrum" help="(-mz_delta) "/>
     <param name="param_algorithm" type="select" optional="False" value="PEPMatrix" label="Algorithm used for consensus scoring" help="(-algorithm) &lt;br&gt;* PEPMatrix: Scoring based on posterior error probabilities (PEPs) and peptide sequence similarities (scored by a substitution matrix). Requires PEPs as scores. &lt;br&gt;* PEPIons: Scoring based on posterior error probabilities (PEPs) and fragment ion similarities ('shared peak count'). Requires PEPs as scores. &lt;br&gt;* best: For each peptide ID, use the best score of any search engine as the consensus score. Requires the same score type in all ID runs. &lt;br&gt;* worst: For each peptide ID, use the worst score of any search engine as the consensus score. Requires the same score type in all ID runs. &lt;br&gt;* average:  For each peptide ID, use the average score of all search engines as the consensus. Requires the same score type in all ID runs. &lt;br&gt;* ranks: Calculates a consensus score based on the ranks of peptide IDs in the results of different search engines. The final score is in the range (0, 1], with 1 being the best score. No requirements about score types">