# HG changeset patch
# User galaxyp
# Date 1721112953 0
# Node ID ef46866326ef6ec95d91e1c6bb399338a40b7eac
# Parent  dc5de2ea607ef1ba266ab33cfa0dd58673382e93
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit e75f095a55caa325cd97127114c9703e4557ad50

diff -r dc5de2ea607e -r ef46866326ef macros.xml
--- a/macros.xml	Fri Jul 12 18:16:43 2024 +0000
+++ b/macros.xml	Tue Jul 16 06:55:53 2024 +0000
@@ -1,7 +1,7 @@
 <macros>
     <import>msfragger_macros.xml</import>
     <token name="@TOOL_VERSION@">20.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">fragpipe</requirement>
@@ -20,11 +20,11 @@
       name, experiment, bioreplicate, data type
     -->
     <xml name="samples">
-        <param name="inputs" type="data" format="mzml,mzxml" multiple="true" label="Proteomics Spectrum files"  help="All input scan files must of a matching format: mzML, mzXML"/>
+        <param name="inputs" type="data" format="mzml,mzxml,thermo.raw" multiple="true" label="Proteomics Spectrum files"  help="All input scan files must be named with one of the following extensions: .mzML, .mzXML, or .raw"/>
         <param name="input_prefix" type="text" value="" optional="true" label="File name prefix" help="Names inputs: prefix_rep#.mzXML Leave blank to use History names of inputs">
               <validator type="regex" message="">[a-zA-Z][a-zA-Z0-9_-]*</validator>
         </param>
-        <param name="manifest" type="data" format="tabular" label="Manifest file" help="TSV file with entries for each input scan file: Name (Name of input Galaxy history item. Extension in the name must be mzML or mzXML.), Experiment (empty, alphanumeric, or _), Bioreplicate (empty or integer), Data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-lib)"/>
+        <param name="manifest" type="data" format="tabular" label="Manifest file" help="TSV file with entries for each input scan file: Name (Name of input Galaxy history item. Extension in the name must be .mzML, .mzXML, or .raw.), Experiment (empty, alphanumeric, or _), Bioreplicate (empty or integer), Data type (DDA, DIA, GPF-DIA, DIA-Quant, or DIA-lib)"/>
     </xml>
 
     <!--