# HG changeset patch
# User computational-metabolomics
# Date 1597062589 14400
# Node ID 7856fc53df1daf01a6a4902b551d08e0c207536b
# Parent  1cba235b197236ce152c240e885cfd4e0f6fd8f4
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cbbd708ea1e93b1b1643f6bf6da72af65ffd9950"

diff -r 1cba235b1972 -r 7856fc53df1d README.rst
--- a/README.rst	Thu Apr 09 14:15:03 2020 -0400
+++ b/README.rst	Mon Aug 10 08:29:49 2020 -0400
@@ -3,13 +3,13 @@
 |Build Status (Travis)| |Git| |Bioconda| |License|
 
 
-Version v1.12.2+galaxy1
+Version v1.12.2+galaxy2
 ------
 
   - msPurity
      - bioconductor-mspurity v1.12.2
   - Galaxy tools
-     - v1
+     - v2
 
 About
 ------
@@ -55,6 +55,11 @@
 
 Changes
 -------------------------
+v1.12.2-galaxy2
+  - Bug fix for using custom library sqlite database from Galaxy UI
+  - Bug fix for "allfrag" for createDatabase
+
+
 v1.12.2-galaxy1
   - grpPeaklist reference incorrect in createDatabase.xml
   - Add custom adduct handling for createMSP
diff -r 1cba235b1972 -r 7856fc53df1d createDatabase.R
--- a/createDatabase.R	Thu Apr 09 14:15:03 2020 -0400
+++ b/createDatabase.R	Mon Aug 10 08:29:49 2020 -0400
@@ -94,7 +94,11 @@
 
 print(pa@fileList)
 
-
+# Missing list element causes failures (should be updated
+# in msPurity R package for future releases)
+if (!exists('allfrag', where=pa@filter_frag_params)){
+    pa@filter_frag_params$allfrag <- FALSE
+}
 
 if (opt$xcms_camera_option=='xcms'){
 
diff -r 1cba235b1972 -r 7856fc53df1d macros.xml
--- a/macros.xml	Thu Apr 09 14:15:03 2020 -0400
+++ b/macros.xml	Mon Aug 10 08:29:49 2020 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.12.2</token>
-    <token name="@GALAXY_TOOL_VERSION@">1</token>
+    <token name="@GALAXY_TOOL_VERSION@">2</token>
 
     <xml name="requirements">
         <requirements>
diff -r 1cba235b1972 -r 7856fc53df1d spectralMatching.R
--- a/spectralMatching.R	Thu Apr 09 14:15:03 2020 -0400
+++ b/spectralMatching.R	Mon Aug 10 08:29:49 2020 -0400
@@ -292,6 +292,7 @@
 q_check <- checkSPeakMeta(opt$q_dbPth, 'query')
 l_check <- checkSPeakMeta(opt$l_dbPth, 'library')
 
+
 if (q_check && l_check){
     sm <- msPurity::spectralMatching(
         q_purity =  opt$q_purity,