--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Apr 09 14:13:16 2020 -0400
@@ -0,0 +1,154 @@
+msPurity for Galaxy
+========================
+|Build Status (Travis)| |Git| |Bioconda| |License|
+
+
+Version v1.12.2+galaxy1
+------
+
+  - msPurity
+     - bioconductor-mspurity v1.12.2
+  - Galaxy tools
+     - v1
+
+About
+------
+Galaxy tools for the Bioconductor R package msPurity. Tools available for assessing precursor ion purity of
+LC-MS/MS or DI-M/MS data that has been acquired. And tools are available to assess LC-MS or DI-MS for
+anticipated precursor ion purity to guide a later fragmentation experiment.
+
+Additional, tools available to perform LC-MS/MS spectral matching.
+
+Associated paper `msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based Fragmentation in Metabolomics. Analytical Chemistry <http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b04358>`_
+
+Use the following links for more details of the msPurity R package:
+
+* Bioconductor: http://bioconductor.org/packages/msPurity/
+* Vignette: https://bioconductor.org/packages/devel/bioc/vignettes/msPurity/inst/doc/msPurity-vignette.html
+* Manual: http://bioconductor.org/packages/devel/bioc/manuals/msPurity/man/msPurity.pdf
+* Bioconductor mirror code: https://github.com/Bioconductor-mirror/msPurity
+* Github code: https://github.com/computational-metabolomics/mspurity
+* Bioconda (stable): https://anaconda.org/bioconda/bioconductor-mspurity
+* Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity
+
+
+
+
+Dependencies
+------
+Dependencies for these Galaxy tools should be handled by CONDA. The most recent version of the msPurity R package can found on channel  `tomnl <https://anaconda.org/tomnl/bioconductor-mspurity>`_ on `anaconda <https://anaconda.org/tomnl/bioconductor-mspurity>`_. Warning this will be a different version of the package compared to the BICONDA bioconductor-mspurity.
+
+
+Galaxy
+------
+`Galaxy <https://galaxyproject.org>`_ is an open, web-based platform for data intensive biomedical research. Whether on the free public server or your own instance, you can perform, reproduce, and share complete analyses.
+
+
+Authors, contributors & contacts
+-------------------------
+
+- Thomas N. Lawson (t.n.lawson@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
+- Ralf J. M. Weber (r.j.weber@bham.ac.uk) - `University of Birmingham (UK) <http://www.birmingham.ac.uk/index.aspx>`_
+- Jordi Capellades (j.capellades.to@gmail.com) - `Universitat Rovira i Virgili (SP)  <http://www.urv.cat/en/>`_
+- Julien Saint-Vanne (jsaintvanne) - `ABiMS (France) <http://abims.sb-roscoff.fr/>`_
+- Simon Bray (sbray@informatik.uni-freiburg.de) - `University of Freiburg (Germany) <https://www.uni-freiburg.de/>`_
+
+Changes
+-------------------------
+v1.12.2-galaxy1
+  - grpPeaklist reference incorrect in createDatabase.xml
+  - Add custom adduct handling for createMSP
+  - Change output of flagRemove to tabular
+
+
+v1.12.2-galaxy0
+  - Update to version v1.12.2 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
+  - Optional summary output for combineAnnotations (for very large output)
+  - Extra column added to flagRemove output
+  - Hide probmetab input 
+  - Make dimsPredictPuritySingle more compatible with "simple workflow inputs"
+
+
+v1.12.1-galaxy0
+  - Update to version v1.12.1 of `msPurity <https://github.com/computational-metabolomics/msPurity/pull/71>`_
+
+v1.12.0-galaxy1
+  - Bug fix (offsets were not being automatically selected for purityA) thanks jsaintvanne
+  - Exit script without error for flagRemove
+  - Username updated in Toolshed yaml
+
+v1.12.0-galaxy0
+  - Updates for Bioconductor stable msPurity v1.12.0 release 
+  - Additional columns added for spectral matching (for msnpy use case)
+  - Merge of v1.11.4-galaxy1
+
+v1.11.4-galaxy1
+  - Not submitted to toolshed
+  - Update to follow IUC guidelines for Galaxy tool development
+
+v1.11.4-galaxy0.2.7
+  - submitted to test toolshed (20190927)
+  - Bug fix for spectralMatching choice of instrument types
+
+v1.11.4-galaxy0.2.6:
+  - submitted to test toolshed (20190924)
+  - 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
+  - Complete update of combineAnnotation tool to use either sqlite, postgres or mysql database
+  - Update of spectralMatching tool to use either sqlite, postgres or mysql database
+  - Added include_adducts parameter to createMSP
+
+v1.11.3-galaxy0.2.5:
+  - Note: This was not pushed to test toolshed
+  - Clean up of the versioning to be in line with IUC
+  - All tools updated with the same versioning
+  - Bump to msPurity v1.11.3 to so EIC is calculated for all features
+
+v0.2.5 (spectralMatching):
+  - spectralMatching - Extra details from matched library spectra is now added to the database (fix)
+
+v0.2.4 (all tools):
+  - bioconductor-mspurity v1.11.2 now used. Fixes EIC problems for MS/MS data
+
+v0.2.2 (spectralMatching):
+  - spectralMatching - Extra details from matched library spectra is now added to the database
+
+v0.2.3 (createDatabase):
+  - createDatabase.xml fix for EIC creation
+
+v0.2.2 (createDatabase, flagRemove, combineAnnotation):
+  - createDatabase.xml fix for xcms3 and CAMERA
+  - flagRemove xcms3 fix
+  - combineAnnotation Made sirius, probmetab and metfrag optional
+  - combineAnnotation fix column sirius
+
+v0.2.1 (all tools):
+  - Update msPurity R code version (bug fix for createMSP and xcms3 version check for createDatabase)
+
+v0.2.0 (all tools):
+  - Update all tools to be more consistent with msPurity core code
+
+License
+-------
+Released under the GNU General Public License v3.0 (see `LICENSE file <https://github.com/computational-metabolomics/dimspy-galaxy/blob/master/LICENSE>`_)
+
+
+.. |Build Status (Travis)| image:: https://img.shields.io/travis/computational-metabolomics/mspurity-galaxy.svg?style=flat&maxAge=3600&label=Travis-CI
+   :target: https://travis-ci.org/computational-metabolomics/mspurity-galaxy
+
+.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=3600
+   :target: https://github.com/computational-metabolomics/mspurity-galaxy
+
+.. |Bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat&maxAge=3600
+   :target: http://bioconda.github.io/recipes/bioconductor-mspurity/README.html
+
+.. |License| image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg
+   :target: https://www.gnu.org/licenses/gpl-3.0.html
+
+

--- a/createMSP.R	Wed Apr 01 10:59:47 2020 -0400
+++ b/createMSP.R	Thu Apr 09 14:13:16 2020 -0400
@@ -15,6 +15,7 @@
   make_option("--intensity_ra",type="character"),
   make_option("--include_adducts",type="character"),
   make_option("--msp_schema",type="character"),
+  make_option("--include_adducts_custom",type="character", default=""),
   make_option("--out_dir",type="character", default=".")
 )
 opt <- parse_args(OptionParser(option_list=option_list))
@@ -66,17 +67,33 @@
   xcms_groupids <- trimws(strsplit(opt$xcms_groupids, ',')[[1]])
 }
 
+
+
+
+
+if (is.null(opt$include_adducts_custom)){
+  include_adducts_custom <- ''
+}else{
+  include_adducts_custom <- opt$include_adducts_custom
+}
+
+
 if (opt$include_adducts=='None'){
   include_adducts <- ''
 }else{
   include_adducts <- opt$include_adducts
-  include_adducts <- gsub("__ob__", "[", include_adducts)
-  include_adducts <- gsub("__cb__", "]", include_adducts)
-  include_adducts <- trimws(include_adducts)
+}
+
+include_adducts_all <- paste(include_adducts_custom, ',', include_adducts, sep="")
 
-  include_adducts <- gsub(",", " ", include_adducts)
+include_adducts_all <- gsub("^,", "", include_adducts_all)
+include_adducts_all <- gsub(",$", "", include_adducts_all)
 
-}
+include_adducts_all <- gsub("__ob__", "[", include_adducts_all)
+include_adducts_all <- gsub("__cb__", "]", include_adducts_all)
+include_adducts_all <- trimws(include_adducts_all)
+include_adducts_all <- gsub(",", " ", include_adducts_all)
+
 
 
 if(is.null(opt$filter)){
@@ -96,7 +113,7 @@
                     xcms_groupids = xcms_groupids,
                     filter = filter,
                     intensity_ra=opt$intensity_ra,
-                    include_adducts=include_adducts,
+                    include_adducts=include_adducts_all,
                     msp_schema=opt$msp_schema)
 
 print('msp created')

--- a/flagRemove.xml	Wed Apr 01 10:59:47 2020 -0400
+++ b/flagRemove.xml	Thu Apr 09 14:13:16 2020 -0400
@@ -149,9 +149,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="peaklist_filtered" format="tsv" label="${tool.name} on ${on_string}: peaklist_filtered (tsv)"
+        <data name="peaklist_filtered" format="tabular" label="${tool.name} on ${on_string}: peaklist_filtered (tsv)"
               from_work_dir="peaklist_filtered.tsv" />
-        <data name="removed_peaks" format="tsv" label="${tool.name} on ${on_string}: removed_peaks (tsv)"
+        <data name="removed_peaks" format="tabular" label="${tool.name} on ${on_string}: removed_peaks (tsv)"
               from_work_dir="removed_peaks.tsv" />
         <data name="xset_filtered" format="rdata" label="xset_filtered"
               from_work_dir="xset_filtered.RData"/>

--- a/macros.xml	Wed Apr 01 10:59:47 2020 -0400
+++ b/macros.xml	Thu Apr 09 14:13:16 2020 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.12.2</token>
-    <token name="@GALAXY_TOOL_VERSION@">0</token>
+    <token name="@GALAXY_TOOL_VERSION@">1</token>
 
     <xml name="requirements">
         <requirements>
@@ -16,6 +16,9 @@
         </requirements>
     </xml>
 
+    <xml name="text-adduct-regex-validator">
+	    <validator type="regex" message="Value may include alphanumeric characters, white space, commas, +, -, [ or ] ">[A-Za-z0-9,\[\] \+\-]+</validator>
+    </xml>
 
     <xml name="offsets">
         <param argument="--minoffset" type="float" label="minoffset" value="0.5"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/createMSP_output_av_all_metadata_custom_adducts.msp	Thu Apr 09 14:13:16 2020 -0400
@@ -0,0 +1,108 @@
+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+NH4]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
+isotope [4][M]+
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+NH4]+
+AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
+CH$LINK: PUBCHEM CID:5328
+CH$NAME Unknown
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+112.050884246826	502873.46875	100
+126.53768157959	2499.31469726562	0.5
+
+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+H+NH3]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
+isotope [4][M]+
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
+AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
+CH$LINK: PUBCHEM CID:5328
+CH$NAME Unknown
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+112.050884246826	502873.46875	100
+126.53768157959	2499.31469726562	0.5
+
+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
+isotope [4][M]+
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+]+
+AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
+CH$LINK: PUBCHEM CID:5328
+CH$NAME Unknown
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+112.050884246826	502873.46875	100
+126.53768157959	2499.31469726562	0.5
+
+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M-H]-
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
+isotope [4][M]+
+MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-
+AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
+CH$LINK: PUBCHEM CID:5328
+CH$NAME Unknown
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+112.050884246826	502873.46875	100
+126.53768157959	2499.31469726562	0.5
+
+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:[M+TEST
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
+isotope [4][M]+
+MS$FOCUSED_ION: PRECURSOR_TYPE [M+TEST
+AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
+CH$LINK: PUBCHEM CID:5328
+CH$NAME Unknown
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+112.050884246826	502873.46875	100
+126.53768157959	2499.31469726562	0.5
+
+RECORD_TITLE: MZ:112.0508 | RT:67.5 | grpid:12 | file:NA | adduct:SPACE+]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050766766484
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.47903
+isotope [4][M]+
+MS$FOCUSED_ION: PRECURSOR_TYPE SPACE+]+
+AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
+AC$MASS_SPECTROMETRY: ION_MODE POSITIVE
+AC$MASS_SPECTROMETRY: MS_TYPE MS2
+CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
+CH$LINK: PUBCHEM CID:5328
+CH$NAME Unknown
+XCMS groupid (grpid): 12
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.12.2 
+PK$NUM_PEAK: 2
+PK$PEAK: m/z int. rel.int.
+112.050884246826	502873.46875	100
+126.53768157959	2499.31469726562	0.5
+