v1.12.2+galaxy2 (#40)

* createDatabase and spectralMatching bug fixes

* Update .travis.yml

* Version bump in readme

* Remove galaxy version for lint travis

Author: Tomnl

.travis.yml

@@ -1,5 +1,5 @@
 language: python
-python: 2.7
+python: 3.7
 cache:
  directories:
   - $HOME/miniconda3
@@ -27,6 +27,6 @@ before_install:
 
 
 script:
-- planemo lint ${TRAVIS_BUILD_DIR}/${TEST}
-- planemo test  --conda_debug  ${TRAVIS_BUILD_DIR}/${TEST}
+- planemo lint ${TRAVIS_BUILD_DIR}/${TEST} 
+- planemo test  --conda_debug  ${TRAVIS_BUILD_DIR}/${TEST} --galaxy_python_version 3.7
 

README.rst

@@ -3,13 +3,13 @@ msPurity for Galaxy
 |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 @@ Authors, contributors & contacts
 
 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

tools/msPurity/createDatabase.R

@@ -94,7 +94,11 @@ pa <- loadRData(opt$pa, 'pa')
 
 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'){
 

tools/msPurity/macros.xml

@@ -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>

tools/msPurity/spectralMatching.R

@@ -292,6 +292,7 @@ if(!is.null(opt$q_rtrangeMin)){
 q_check <- checkSPeakMeta(opt$q_dbPth, 'query')
 l_check <- checkSPeakMeta(opt$l_dbPth, 'library')
 
+
 if (q_check && l_check){
     sm <- msPurity::spectralMatching(
         q_purity =  opt$q_purity,

tools/msPurity/spectralMatching.xml

@@ -19,7 +19,7 @@
 
             #if $Library.l_dbPth_con.l_dbPth_select == 'msPurityData'
               --l_defaultDb
-            #else if $Library.l_dbPth_con.l_dbPth_select == 'userdb_sqlite'
+            #else if $Library.l_dbPth_con.l_dbPth_select == 'sqlite'
               --l_dbPth=$Library.l_dbPth_con.l_dbPth
             #end if