From 94f746247c464fb270358421399810d8a9fb9e8a Mon Sep 17 00:00:00 2001
From: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Date: Fri, 13 Sep 2024 14:18:12 +0100
Subject: [PATCH] v1.28.0+galaxy1 (Galaxy tool fixes for purityX and purityA) -
 doc update (#58)

* Filename fix for purityA output

* Fix for purityX xset object read

* Update pr.yaml

* Update pr.yaml - version bump for upload artifact

* Update pr.yaml artifact version bump

* Update filterFragSpectra.R - update filenames - ensure as character

* Update filterFragSpectra.R - revert - not required

* Update pr.yaml - version bump actions

* Update purityX.xml - update xml wrapper to remove ref to xcms object name

* clean up

* version bump and doc update
---
 tools/msPurity/macros.xml  | 2 +-
 tools/msPurity/purityX.xml | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/msPurity/macros.xml b/tools/msPurity/macros.xml
index 3d41a6d..ec891d1 100644
--- a/tools/msPurity/macros.xml
+++ b/tools/msPurity/macros.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.28.0</token>
-    <token name="@GALAXY_TOOL_VERSION@">0</token>
+    <token name="@GALAXY_TOOL_VERSION@">1</token>
 
     <xml name="requirements">
         <requirements>
diff --git a/tools/msPurity/purityX.xml b/tools/msPurity/purityX.xml
index 403d870..fad5564 100644
--- a/tools/msPurity/purityX.xml
+++ b/tools/msPurity/purityX.xml
@@ -117,10 +117,10 @@
         <expand macro="camera_xcms" />
 
         <param argument="--raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
-               help="Only applicable when using retention time correction with obiwarp. When obiwarp is used
-                     the retention time correction tracking is slightly different to the other correction methods. To ensure
-                     correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to
-                     any retention time correction."/>
+               help="[Deprecated] No longer applicable. Previously when obiwarp was used
+                     the retention time correction tracking was slightly different to the other correction methods. To ensure
+                     correct tracking with obiwarp an additional tool (track_rt_raw) was performed prior to
+                     any retention time correction - and this was then checked when this flag was turned on"/>
 
         <expand macro="fileload" />