Mercurial > repos > tomnl > mspurity_spectralmatching

changeset 13:8dd98b0f83af draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 4f88143938cc198436c2691443832c87e2c31cd0
author tomnl
date Tue, 24 Sep 2019 07:49:51 -0400
parents e131f2fb0f97
children 499c26566a7a
files combineAnnotations.R macros.xml spectralMatching.xml
diffstat 3 files changed, 41 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/combineAnnotations.R	Fri Sep 13 11:48:31 2019 -0400
+++ b/combineAnnotations.R	Tue Sep 24 07:49:51 2019 -0400
@@ -67,7 +67,7 @@
   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 @@
 
 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,
--- a/macros.xml	Fri Sep 13 11:48:31 2019 -0400
+++ b/macros.xml	Tue Sep 24 07:49:51 2019 -0400
@@ -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=""
--- a/spectralMatching.xml	Fri Sep 13 11:48:31 2019 -0400
+++ b/spectralMatching.xml	Tue Sep 24 07:49:51 2019 -0400
@@ -174,7 +174,7 @@
         <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>
 
@@ -182,7 +182,7 @@
         <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>