# HG changeset patch
# User computational-metabolomics
# Date 1644328923 0
# Node ID 2e10c13085c9ad53e2b27525cdd023805daa14e0
# Parent  cc0f8ddad4a833c01688842d90b84c7cbe95c5a2
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"

diff -r cc0f8ddad4a8 -r 2e10c13085c9 README.rst
--- a/README.rst	Thu Mar 04 12:28:18 2021 +0000
+++ b/README.rst	Tue Feb 08 14:02:03 2022 +0000
@@ -3,13 +3,13 @@
 |Build Status (Travis)| |Git| |Bioconda| |License|
 
 
-Version v1.16.2+galaxy0
+Version v1.16.2+galaxy1
 ------------------------
 
   - msPurity
      - bioconductor-mspurity v1.16.2
   - Galaxy tools
-     - v0
+     - v1
 
 About
 ------
@@ -32,8 +32,6 @@
 * Conda (dev and testing): https://anaconda.org/tomnl/bioconductor-mspurity
 
 
-
-
 Dependencies
 ------------------
 Dependencies for these Galaxy tools should be handled by CONDA.
@@ -53,8 +51,13 @@
 - 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
 -------------------------
+v1.16.2-galaxy1
+  - Fix for "scan" option for spectral matching
+  - Add allfrag option for filterFragSpectra
+
 v1.16.2-galaxy0
   - Version bump
   - Fix for intra spectral matching
diff -r cc0f8ddad4a8 -r 2e10c13085c9 filterFragSpectra.R
--- a/filterFragSpectra.R	Thu Mar 04 12:28:18 2021 +0000
+++ b/filterFragSpectra.R	Tue Feb 08 14:02:03 2022 +0000
@@ -17,7 +17,8 @@
   make_option("--snr", default = 0.0),
 
   make_option("--rmp", action = "store_true"),
-  make_option("--snmeth", default = "median", type = "character")
+  make_option("--snmeth", default = "median", type = "character"),
+  make_option("--allfrag", action = "store_true")
 )
 
 opt <- parse_args(OptionParser(option_list = option_list))
@@ -39,12 +40,19 @@
   opt$rmp <- TRUE
 }
 
+if (is.null(opt$allfrag)) {
+  opt$allfrag <- FALSE
+}else{
+  opt$allfrag <- TRUE
+}
+
 pa <- filterFragSpectra(pa,
                         ilim = opt$ilim,
                         plim = opt$plim,
                         ra = opt$ra,
                         snr = opt$snr,
                         rmp = opt$rmp,
+                        allfrag = opt$allfrag,
                         snmeth = opt$snmeth)
 
 print(pa)
diff -r cc0f8ddad4a8 -r 2e10c13085c9 filterFragSpectra.xml
--- a/filterFragSpectra.xml	Thu Mar 04 12:28:18 2021 +0000
+++ b/filterFragSpectra.xml	Tue Feb 08 14:02:03 2022 +0000
@@ -18,6 +18,7 @@
             --snr=$snr
             --snmeth=$snmeth
             $rmp
+            $allfrag
     ]]></command>
     <inputs>
         <param argument="--pa" type="data"
@@ -40,6 +41,9 @@
                label="Remove peaks that do not meet the filtering criteria.
                       Otherwise peaks will be flagged instead."
                help="" />
+        <param argument="--allfrag" type="boolean" checked="false" truevalue="--allfrag" falsevalue=""
+               label="Perform filtering on all fragmentation spectra (not just those aligned to XCMS features)"
+               help="" />
     </inputs>
     <outputs>
         <data name="filterFragSpectra_output_rdata" format="rdata"
diff -r cc0f8ddad4a8 -r 2e10c13085c9 macros.xml
--- a/macros.xml	Thu Mar 04 12:28:18 2021 +0000
+++ b/macros.xml	Tue Feb 08 14:02:03 2022 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.16.2</token>
-    <token name="@GALAXY_TOOL_VERSION@">0</token>
+    <token name="@GALAXY_TOOL_VERSION@">1</token>
 
     <xml name="requirements">
         <requirements>
@@ -271,7 +271,7 @@
                         <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="FD-B">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>
@@ -333,13 +333,14 @@
 
             <conditional name="@QL_SHRT@_spectraTypes_cond">
                 <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
-                help="" />
+                help="Note that when using 'scan' spectra types the spectraFilter option may need to be FALSE 
+		      if 'allfrag' was not selecting when performing filterFragSpectra or if no filtering was performed at all" />
                 <when value="true">
                     <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true"  label="Spectra type" >
                         <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
                         <option value="inter">Averaged inter spectra</option>
                         <option value="intra">Averaged intra spectra </option>
-                        <option value="scans">All individual scans</option>
+                        <option value="scan">All individual scans (may need to set spectraFilter to false with this option)</option>
                         <option value="NA">Not applicable/defined</option>
                     </param>
                 </when>