# HG changeset patch
# User galaxyp
# Date 1502213054 14400
# Node ID aef076574eab8ad03bffd3236f272838767015ae
# Parent  872ffe5b42306285f3bf870cd02e1bcdd9de62cb
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8fcd33df23901e111d6c18f450bd09cd8cb3819e

diff -r 872ffe5b4230 -r aef076574eab OpenSwathWorkflow.xml
--- a/OpenSwathWorkflow.xml	Mon Aug 07 14:47:06 2017 -0400
+++ b/OpenSwathWorkflow.xml	Tue Aug 08 13:24:14 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: [Utilities]-->
-<tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.2.0">
+<tool id="OpenSwathWorkflow" name="OpenSwathWorkflow" version="2.2.0.1">
   <description>Complete workflow to run OpenSWATH</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathWorkflow</token>
@@ -466,7 +466,7 @@
     <param name="param_outlierDetection_MinBinsFilled" type="integer" value="8" label="Minimal number of bins required to be covered" help="(-MinBinsFilled) "/>
     <expand macro="advanced_options">
       <param name="param_rt_norm" type="data" format="trafoxml" optional="True" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help="(-rt_norm) If set, tr_irt may be omitted"/>
-      <param name="param_swath_windows_file" type="data" format="text" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
+      <param name="param_swath_windows_file" type="data" format="txt" label="Optional, tab separated file containing the SWATH windows for extraction: lower_offset upper_offset \newline 400 425 \newline .." help="(-swath_windows_file) Note that the first line is a header and will be skipped"/>
       <param name="param_sort_swath_maps" display="radio" type="boolean" truevalue="-sort_swath_maps" falsevalue="" checked="false" optional="True" label="Sort of input SWATH files when matching to SWATH windows from swath_windows_file" help="(-sort_swath_maps) "/>
       <param name="param_use_ms1_traces" display="radio" type="boolean" truevalue="-use_ms1_traces" falsevalue="" checked="false" optional="True" label="Extract the precursor ion trace(s) and use for scoring" help="(-use_ms1_traces) "/>
       <param name="param_enable_uis_scoring" display="radio" type="boolean" truevalue="-enable_uis_scoring" falsevalue="" checked="false" optional="True" label="Enable additional scoring of identification assays" help="(-enable_uis_scoring) "/>