v1.11.4+galaxy0.2.6 (#26)

* Ensure correct compoundDbPth used * Update link the database schema * Update sql references for docs, version bump * Update instrument type selection * msp_split tool update * update of tests for msp_split * update travis * Update readme
computational-metabolomics · Sep 24, 2019 · 4f88143 · 4f88143
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commit 4f88143
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diff --git a/.travis.yml b/.travis.yml
@@ -16,7 +16,7 @@ env:
   - TEST=tools/msPurity/flagRemove.xml
   - TEST=tools/msPurity/frag4feature.xml
   - TEST=tools/msPurity/purityX.xml
-  - TEST=tools/utils/msp_split.xml
+  - TEST=tools/utils/msp_split/msp_split.xml
   - TEST=tools/utils/submit_to_mogi.xml
 
 

diff --git a/README.rst b/README.rst
@@ -6,14 +6,14 @@ Warning
 ------
 Proceed with caution these tools are in active development so tools may change! Stable release to Galaxy toolshed coming soon. Currently these tools will only work when the 'tomnl' conda channel is being used with Galaxy.
 
-Version v1.11.4-galaxy0.2.5
+Version v1.11.4+galaxy0.2.6
 ------
 NOTE: bioconductor-mspurity v1.11.4 only available on 'tomnl' conda channel - to be updated to bioconda soon.
 
   - msPurity
      - bioconductor-mspurity v1.11.4
   - Galaxy tools
-     - v0.2.5
+     - v0.2.6
 
 About
 ------
@@ -58,6 +58,13 @@ Authors, contributors & contacts
 
 Changes
 -------------------------
+v1.11.4-galaxy0.2.6:
+  - submitted to test toolshed (xx)
+  - Bug fix for createAnnotation database local path
+  - Update of instrument types for spectral matching
+  - Update of split_msp tool to handle different MSP types
+
+
 v1.11.4-galaxy0.2.5:
   - submitted to test toolshed (20190913)
   - Added ppmInterp parameter to purityA

diff --git a/tools/msPurity/combineAnnotations.R b/tools/msPurity/combineAnnotations.R
@@ -67,7 +67,7 @@ if (opt$compoundDbType=='local_config'){
   source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
   source_local("dbconfig.R")
 }else{
-  compoundDbType = opt$compoundDbType
+  compoundDbType = compoundDbType
   compoundDbName = NA
   compoundDbHost = NA
   compoundDbPort = NA
@@ -79,7 +79,7 @@ if (opt$compoundDbType=='local_config'){
 
 summary_output <- msPurity::combineAnnotations(
                             sm_resultPth = sm_resultPth,
-                            compoundDbPth = opt$compoundDbPth,
+                            compoundDbPth = compoundDbPth,
                             metfrag_resultPth = opt$metfrag_resultPth,
                             sirius_csi_resultPth = opt$sirius_csi_resultPth,
                             probmetab_resultPth = opt$probmetab_resultPth,

diff --git a/tools/msPurity/macros.xml b/tools/msPurity/macros.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.11.4</token>
-    <token name="@GALAXY_TOOL_VERSION@">0.2.5</token>
+    <token name="@GALAXY_TOOL_VERSION@">0.2.6</token>
 
     <xml name="requirements">
         <requirements>
@@ -108,7 +108,7 @@
         <conditional name="@QL_SHRT@_dbPth_con">
             <param name="@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" >
                 <option value="sqlite" selected="@USER@" >SQLite database of (LC)-MS/MS data</option>
-                <option value="local_config" selected="@USER@" >Locally configured MySQL or Postgres database</option>
+                <option value="local_config" selected="@USER@" >Locally configured SQLite, MySQL or PostgreSQL database</option>
                 <option value="msPurityData"  selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option>
             </param>
             <when value="sqlite">
@@ -248,36 +248,59 @@
                 <when value="true">
                     <param name="@QL_SHRT@_instrumentTypes" type="select" multiple="true"
                        help="" >
-                        <option value="APCI-ITFT">APCI-ITFT</option>
-                        <option value="CE-ESI-TOF" selected="true">CE-ESI-TOF</option>
+                        <option value="APCI-ITFT" selected="true" >APCI-ITFT</option>
+                        <option value="APCI-ITTOF" selected="true" >APCI-ITTOF</option>
+                        <option value="CE-ESI-TOF" selected="true" >CE-ESI-TOF</option>
                         <option value="CI-B">CI-B</option>
                         <option value="EI-B">EI-B</option>
                         <option value="EI-EBEB">EI-EBEB</option>
-                        <option value="ESI-ITFT" selected="true">ESI-ITFT</option>
-                        <option value="ESI-ITTOF" selected="true">ESI-ITTOF</option>
-                        <option value="ESI-QTOF" selected="true">ESI-QTOF</option>
+                        <option value="ESI-ITFT" selected="true" >ESI-ITFT</option>
+                        <option value="ESI-ITTOF" selected="true" >ESI-ITTOF</option>
+                        <option value="ESI-QFT" selected="true" >ESI-QFT</option>
+                        <option value="ESI-QTOF" selected="true" >ESI-QTOF</option>
+                        <option value="ESI-TOF" selected="true" >ESI-TOF</option>
                         <option value="FAB-B">FAB-B</option>
-                        <option value="FAB-BE-MS">FAB-BE-MS</option>
+                        <option value="FAB-BE">FAB-BE</option>
                         <option value="FAB-EB">FAB-EB</option>
                         <option value="FAB-EBEB">FAB-EBEB</option>
+                        <option value="FAB-EBEB">FD-B</option>
                         <option value="FI-B">FI-B</option>
+                        <option value="Flow-injection QqQ/MS">Flow-injection QqQ/MS</option>
                         <option value="GC-EI-Q">GC-EI-Q</option>
                         <option value="GC-EI-QQ">GC-EI-QQ</option>
                         <option value="GC-EI-TOF">GC-EI-TOF</option>
-                        <option value="LC-APCI-QTOF">LC-APCI-QTOF</option>
+                        <option value="GC-MS">GC-MS</option>
+                        <option value="Hybrid FT">Hybrid FT</option>
+                        <option value="in source CID" selected="true" >in source CID</option>
+                        <option value="In-silico QTOF" selected="true" >In-silico QTOF</option>
+                        <option value="Ion trap" selected="true" >Ion trap</option>
+                        <option value="LC-APCI-ITFT" selected="true" >LC-APCI-ITFT</option>
+                        <option value="LC-APCI-QTOF" selected="true" >LC-APCI-QTOF</option>
+                        <option value="LC-APCI-Q" selected="true">LC-APCI-Q</option>
                         <option value="LC-APPI-QQ">LC-APPI-QQ</option>
                         <option value="LC-ESI-IT" selected="true">LC-ESI-IT</option>
                         <option value="LC-ESI-ITFT" selected="true">LC-ESI-ITFT</option>
                         <option value="LC-ESI-ITTOF" selected="true">LC-ESI-ITTOF</option>
-                        <option value="LC-ESI-Q">LC-ESI-Q</option>
-                        <option value="LC-ESI-QFT" selected="true" >LC-ESI-QFT</option>
+                        <option value="LC-ESI-Q" selected="true">LC-ESI-Q</option>
+                        <option value="LC-ESI-QFT" selected="true">LC-ESI-QFT</option>
                         <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option>
                         <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option>
                         <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option>
                         <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option>
-                        <option value="MALDI-QIT">MALDI-QIT</option>
-                        <option value="MALDI-TOF">MALDI-TOF</option>
-                        <option value="ALDI-TOFTOF">ALDI-TOFTOF</option>
+                        <option value="LC-Q-TOF/MS" selected="true">LC-Q-TOF/MS</option>
+                        <option value="LC-QTOF" selected="true">LC-QTOF</option>
+                        <option value="Linear Ion Trap" selected="true">Linear Ion Trap</option>
+                        <option value="LIT" selected="true">LIT</option>
+                        <option value="MALDI-QIT" selected="true">MALDI-QIT</option>
+                        <option value="MALDI-TOF" selected="true">MALDI-TOF</option>
+                        <option value="MALDI-TOFTOF" selected="true">MALDI-TOFTOF</option>
+                        <option value="orbitrap" selected="true">orbitrap</option>
+                        <option value="QIT" selected="true">QIT</option>
+                        <option value="QIT-FT" selected="true">QIT-FT</option>
+                        <option value="QIT-TOF" selected="true">QIT-TOF</option>
+                        <option value="QqQ" selected="true">QqQ</option>
+                        <option value="Q-TOF" selected="true">Q-TOF</option>
+                        <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option>
                         <option value="none">None</option>
                   </param>
                   <param name="@QL_SHRT@_instrumentTypesUser" type="text" value=""

diff --git a/tools/msPurity/spectralMatching.xml b/tools/msPurity/spectralMatching.xml
@@ -174,15 +174,15 @@
         <expand macro="sm_input" ql='Query' ql_shrt = "q" user="True" mspuritydatalib="False" msp="False"
                 help="Query SQLite database - in the standard XCMS msPurity workflow - the output
                       of msPurity.createDatabase should be used here. However any SQLite database
-                      following the schema of xxx can be used as input"/>
+                      following the schema of as https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/>
         <expand macro="filters" ql="Query" ql_shrt="q"/>
     </section>
 
     <section name="Library" title="Library spectra input and filters" expanded="True">
         <expand macro="sm_input" ql='Library' ql_shrt = "l" user="False" mspuritydatalib="True" msp="False"
                 help="Library SQLite database - in the standard XCMS msPurity workflow - a default
                       database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite
-                      database following the schema of xxx can be used as input"/>
+                      database following the schema of https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/>
         <expand macro="filters" ql="Library"  ql_shrt="l"/>
     </section>
 

diff --git a/tools/utils/msp_split/.shed.yml b/tools/utils/msp_split/.shed.yml
@@ -0,0 +1,8 @@
+owner: tomnl
+remote_repository_url: https://github.com/computational-metabolomics/mspurity-galaxy
+homepage_url:  https://github.com/computational-metabolomics/mspurity-galaxy
+categories: ["Metabolomics"]
+description: "[Metabolomics][LC-MS][DIMS][MS/MS] msPurity -  R package for precursor ion purity assessments, data processing and spectral matching for LC-MS(/MS) and DI-MS(/MS) data"
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "[Metabolomics][LC-MS][DIMS][MS/MS] msPurity - {{ tool_name }} {{description}}"
diff --git a/tools/utils/msp_split.py → tools/utils/msp_split/msp_split.py b/tools/utils/msp_split.py → tools/utils/msp_split/msp_split.py
diff --git a/tools/utils/msp_split.xml → tools/utils/msp_split/msp_split.xml b/tools/utils/msp_split.xml → tools/utils/msp_split/msp_split.xml
diff --git a/tools/utils/test-data/file01.msp → tools/utils/msp_split/test-data/file01.msp b/tools/utils/test-data/file01.msp → tools/utils/msp_split/test-data/file01.msp
diff --git a/tools/utils/test-data/file02.msp → tools/utils/msp_split/test-data/file02.msp b/tools/utils/test-data/file02.msp → tools/utils/msp_split/test-data/file02.msp
diff --git a/tools/utils/test-data/input.msp → tools/utils/msp_split/test-data/input.msp b/tools/utils/test-data/input.msp → tools/utils/msp_split/test-data/input.msp