v1.28.0+galaxy0 (#55)

* version bump

* removed slash github yaml

README.rst

@@ -3,13 +3,13 @@ msPurity for Galaxy
 |Git| |Bioconda| |License|
 
 
-Version v1.16.2+galaxy2
+Version v1.28.0+galaxy0
 ------------------------
 
   - msPurity
-     - bioconductor-mspurity v1.16.2
+     - bioconductor-mspurity v1.28.0
   - Galaxy tools
-     - v2
+     - v0
 
 About
 ------
@@ -26,10 +26,8 @@ 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
@@ -54,6 +52,12 @@ Authors, contributors & contacts
 
 Changes
 -------------------------
+v1.28.0-galaxy0
+  - Version bump to v1.28.0
+  - createMSP now uses the median precursor MZ and precursor RT in the MSP files
+  - flagRemove updated to handle different xcms version objects internally within msPurity R function
+  - Relevant unit tests updated and further tidying up of repo
+
 v1.16.2-galaxy2 
   - Fix for purityX galaxy tool (https://github.com/computational-metabolomics/mspurity-galaxy/issues/53) 
   - Cleanup of xml based on updated lint requirements

tools/msPurity/flagRemove.R

@@ -1,4 +1,5 @@
 library(msPurity)
+library(xcms)
 library(optparse)
 print(sessionInfo())
 option_list <- list(
@@ -117,19 +118,25 @@ if (is.null(opt$remove_spectra)) {
 
 print(opt)
 
-getxcmsSetObject <- function(xobject) {
-    # XCMS 1.x
-    if (class(xobject) == "xcmsSet") {
-        return(xobject)
-    }
-    # XCMS 3.x
-    if (class(xobject) == "XCMSnExp") {
-        # Get the legacy xcmsSet object
-        suppressWarnings(xset <- as(xobject, "xcmsSet"))
-        xcms::sampclass(xset) <- xset@phenoData$sample_group
-        return(xset)
-    }
-}
+# This R function can handle both XCMS object versions (so following code
+# no longer required - kept here for reference)
+# getxcmsSetObject <- function(xobject) {
+#   # XCMS 1.x
+#   if (class(xobject) == "xcmsSet"){
+#     return(xobject)
+#   }
+#   # XCMS 3.x
+#   if (class(xobject) == "XCMSnExp") {
+#     # Get the legacy xcmsSet object
+#     suppressWarnings(xset <- as(xobject, "xcmsSet"))
+#     if (!is.null(xset@phenoData$sample_group)){
+#       xcms::sampclass(xset) <- xset@phenoData$sample_group
+#     }else{
+#       xcms::sampclass(xset) <- "."
+#     }
+#     return(xset)
+#   }
+# }
 
 
 loadRData <- function(rdata_path, name) {
@@ -138,9 +145,9 @@ loadRData <- function(rdata_path, name) {
     return(get(ls()[ls() %in% name]))
 }
 
-xset <- getxcmsSetObject(loadRData(opt$xset_path, c("xset", "xdata")))
+xset <- loadRData(opt$xset_path, c("xset", "xdata"))
+
 
-print(xset)
 if (is.null(opt$samplelist)) {
     blank_class <- opt$blank_class
 } else {
@@ -157,6 +164,8 @@ if (is.null(opt$samplelist)) {
 }
 
 
+
+
 if (is.null(opt$multilist)) {
     ffrm_out <- flag_remove(xset,
         pol = opt$polarity,
@@ -201,15 +210,6 @@ if (is.null(opt$multilist)) {
     )
 } else {
     # nolint start
-    # TODO
-    # xsets <- split(xset, multilist_df$multlist)
-    #
-    # mult_grps <- unique(multilist_df$multlist)
-    #
-    # for (mgrp in mult_grps){
-    #   xset_i <- xsets[mgrp]
-    #   xcms::group(xset_i,
-    #
-    # }
+    # TODO - potential for multilist analysis (e)
     # nolint end
 }

tools/msPurity/frag4feature.R

@@ -81,7 +81,11 @@ getxcmsSetObject <- function(xobject) {
     if (class(xobject) == "XCMSnExp") {
         # Get the legacy xcmsSet object
         suppressWarnings(xset <- as(xobject, "xcmsSet"))
-        sampclass(xset) <- xset@phenoData$sample_group
+        if (!is.null(xset@phenoData$sample_group)) {
+            xcms::sampclass(xset) <- xset@phenoData$sample_group
+        } else {
+            xcms::sampclass(xset) <- "."
+        }
         return(xset)
     }
 }
@@ -96,6 +100,7 @@ pa@cores <- opt$cores
 print(pa@fileList)
 print(xset@filepaths)
 
+
 if (is.null(opt$intense)) {
     intense <- FALSE
 } else {

tools/msPurity/macros.xml

@@ -1,17 +1,17 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.16.2</token>
-    <token name="@GALAXY_TOOL_VERSION@">2</token>
+    <token name="@TOOL_VERSION@">1.28.0</token>
+    <token name="@GALAXY_TOOL_VERSION@">0</token>
 
     <xml name="requirements">
         <requirements>
            <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>
-           <requirement type="package" version="1.46.0" >bioconductor-camera</requirement>
-           <requirement type="package" version="3.12.0" >bioconductor-xcms</requirement>
-           <requirement type="package" version="1.18.0" >bioconductor-mspuritydata</requirement>
-           <requirement type="package" version="1.6.6">r-optparse</requirement>
-           <requirement type="package" version="1.3.1">r-rpostgres</requirement>
-           <requirement type="package" version="0.10.21">r-rmysql</requirement>
+           <requirement type="package" version="1.58.0" >bioconductor-camera</requirement>
+           <requirement type="package" version="4.0.0" >bioconductor-xcms</requirement>
+           <requirement type="package" version="1.30.0" >bioconductor-mspuritydata</requirement>
+           <requirement type="package" version="1.7.5">r-optparse</requirement>
+           <requirement type="package" version="1.4.7">r-rpostgres</requirement>
+           <requirement type="package" version="0.10.27">r-rmysql</requirement>
             <yield />
         </requirements>
     </xml>

tools/msPurity/purityX.R

@@ -74,14 +74,18 @@ loadRData <- function(rdata_path, xset_name) {
 
 getxcmsSetObject <- function(xobject) {
   # XCMS 1.x
-  if (class(xobject) == "xcmsSet") {
+  if (class(xobject) == "xcmsSet"){
     return(xobject)
   }
   # XCMS 3.x
   if (class(xobject) == "XCMSnExp") {
     # Get the legacy xcmsSet object
     suppressWarnings(xset <- as(xobject, "xcmsSet"))
-    sampclass(xset) <- xset@phenoData$sample_group
+    if (!is.null(xset@phenoData$sample_group)){
+      xcms::sampclass(xset) <- xset@phenoData$sample_group
+    }else{
+      xcms::sampclass(xset) <- "."
+    }
     return(xset)
   }
 }

tools/msPurity/test-data/createMSP_output_av_all_metadata.msp

@@ -1,6 +1,6 @@
-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
+RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+NH4]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532
 isotope [4][M]+
 MS$FOCUSED_ION: PRECURSOR_TYPE [M+NH4]+
 AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
@@ -10,15 +10,15 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 
 PK$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
+RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+H+NH3]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532
 isotope [4][M]+
 MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
 AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
@@ -28,7 +28,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100

tools/msPurity/test-data/createMSP_output_av_all_metadata_custom_adducts.msp

@@ -1,6 +1,6 @@
-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
+RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+NH4]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532
 isotope [4][M]+
 MS$FOCUSED_ION: PRECURSOR_TYPE [M+NH4]+
 AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
@@ -10,15 +10,15 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 
 PK$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
+RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+H+NH3]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532
 isotope [4][M]+
 MS$FOCUSED_ION: PRECURSOR_TYPE [M+H+NH3]+
 AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
@@ -28,15 +28,15 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 
 PK$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
+RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532
 isotope [4][M]+
 MS$FOCUSED_ION: PRECURSOR_TYPE [M+]+
 AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
@@ -46,15 +46,15 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 
 PK$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
+RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M-H]-
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532
 isotope [4][M]+
 MS$FOCUSED_ION: PRECURSOR_TYPE [M-H]-
 AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
@@ -64,15 +64,15 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 
 PK$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
+RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:[M+TEST
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532
 isotope [4][M]+
 MS$FOCUSED_ION: PRECURSOR_TYPE [M+TEST
 AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
@@ -82,15 +82,15 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 
 PK$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
+RECORD_TITLE: MZ:112.0508 | RT:67.6 | grpid:12 | file:NA | adduct:SPACE+]+
+MS$FOCUSED_ION: PRECURSOR_M/Z 112.050811228882
+AC$CHROMATOGRAPHY: RETENTION_TIME 67.556532
 isotope [4][M]+
 MS$FOCUSED_ION: PRECURSOR_TYPE SPACE+]+
 AC$CHROMATOGRAPHY: COLUMN_NAME Acclaim RSLC C18 2.2um 2.1x100mm Thermo
@@ -100,7 +100,7 @@ CH$LINK: INCHIKEY VACCAVUAMIDAGB-UHFFFAOYSA-N
 CH$LINK: PUBCHEM CID:5328
 CH$NAME Unknown
 XCMS groupid (grpid): 12
-COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.16.2 
+COMMENT: Exported from msPurity purityA object using function createMSP, using method 'av_all' msPurity version:1.28.0 
 PK$NUM_PEAK: 2
 PK$PEAK: m/z int. rel.int.
 112.050884246826	502873.46875	100