--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spectral_matching.xml	Mon Mar 05 10:03:43 2018 -0500
@@ -0,0 +1,200 @@
+<tool id="spectral_matching" name="spectral_matching" version="0.0.15">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements">
+    </expand>
+
+    <description>
+        Perform spectral matching to spectral libraries using dot product cosine on a MS/MS dataset
+    </description>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="Rscript"><![CDATA[
+        spectral_matching.R
+            --out_dir=.
+            --target_db_pth=$target_db
+            --library_db_pth=$library_db
+            --ra_thres_l=$advanced.ra_thres_l
+            --ra_thres_t=$advanced.ra_thres_t
+            --cores=\${GALAXY_SLOTS:-4}
+            --pol=$pol
+            --score_thres=$score_thres
+            --ppm_tol_prod=$ppm_tol_prod
+            --ppm_tol_prec=$ppm_tol_prec
+            --instrument_types=$instrument_types
+            --library_sources=$library_sources
+            #if $advanced.topncond.topnbool:
+                --topn=$topn
+            #end if
+            #if $advanced.scan_ids:
+              --scan_ids='
+                #for $i, $j in enumerate($advanced.scan_ids)
+                    $j.scan_ids,
+                #end for
+                '
+            #end if
+            #if $create_new_database:
+              --create_new_database
+            #end if
+
+
+
+    ]]></command>
+    <inputs>
+
+        <param type="data" name="target_db" label="SQLite DB of target spectra" format="sqlite"
+               help="SQLite DB of target spectra. (e.g. generated from frag4feature tool)"/>
+
+        <param type="data" name="library_db" label="SQLite DB of library spectra" format="sqlite"
+               help="SQLite database of library (reference) spectra,
+               As a temporary quick solution. The library can be used from this dropbox link
+               https://www.dropbox.com/s/csxj6pairsgd8fe/library_spectra.db?dl=1
+               A more official location can be found here: https://bioconductor.org/packages/release/data/experiment/src/contrib/msPurityData_1.6.0.tar.gz
+                "/>
+
+
+        <param name="pol" type="select" label="polarity" >
+                <option value="positive" selected="true">Positive</option>
+                <option value="negative"  >negative</option>
+        </param>
+
+        <param name="ppm_tol_prod" type="float" value="10"
+                    help="Parts per million tolerance to match product mz values"/>
+
+        <param name="ppm_tol_prec" type="float" value="5"
+                    help="Parts per million tolerance to match precursor mz values"/>
+
+        <param name="score_thres" type="float" min="0" max="1" value="0.6"
+                    help="Dot product cosine score threshold"/>
+
+        <param name="instrument_types" type="select"  multiple="true" >
+            <option value="APCI-ITFT">APCI-ITFT</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="FAB-B">FAB-B</option>
+            <option value="FAB-BE-MS">FAB-BE-MS</option>
+            <option value="FAB-EB">FAB-EB</option>
+            <option value="FAB-EBEB">FAB-EBEB</option>
+            <option value="FI-B">FI-B</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="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-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>
+        </param>
+
+        <param name="library_sources" type="select"  multiple="true" >
+            <option value="lipidblast">LipidBlast</option>
+            <option value="massbank" selected="true">MassBank</option>
+            <option value="GNPS">GNPS</option>
+        </param>
+        <param name="create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
+               help="A copy will be made of the input SQLite target database and the results will be added to this copy.
+                     When False, the input SQLite database will be updated  with the matching results. Use False
+                     if you want to reduce storage space being used."/>
+
+        <section name="advanced" title="advanced" expanded="False">
+            <conditional name="topncond">
+                <param name="topnbool" type="boolean" label="Only use the top n spectral matching hits?"/>
+                <when value="false">
+                </when>
+                <when value="true">
+                     <param name="topn" type="integer" value="10" help="Only use top n matches"/>
+                </when>
+            </conditional>
+
+            <param name="ra_thres_l" type="float" value="0"
+               help="Relative abundance threshold for library spectra"/>
+
+            <param name="ra_thres_t" type="float" value="2"
+               help="Relative abundance threshold for target spectra (e.g. spectral data from users MS files)"/>
+
+            <repeat name="scan_ids" title="Specific scan ids">
+                <param name="scan_ids" type="integer" value=""/>
+            </repeat>
+
+
+        </section>
+
+    </inputs>
+    <outputs>
+
+
+
+	    <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results"
+              from_work_dir="results.sqlite" visible="true">
+            <filter>create_new_database is True</filter>
+        </data>
+        <data name="scan_hits" format="tsv" label="${tool.name} on ${on_string}: scan hits"
+              from_work_dir="scan_hits.tsv" visible="true"/>
+        <data name="xcms_hits" format="tsv" label="${tool.name} on ${on_string}: xcms hits"
+              from_work_dir="xcms_hits.tsv" visible="true"/>
+    </outputs>
+    <tests>
+        <!--<test>-->
+
+            <!--<param name="target_db" value="alldata.sqlite" />-->
+            <!--<param name="library_db" value="https://www.dropbox.com/s/csxj6pairsgd8fe/library_spectra.db?dl=0"/>-->
+            <!--<output name="xcms_hits" value="spectra_matching_xcms_hits.tsv" />-->
+            <!--<output name="scan_hits" value="spectra_matching_scan_hits.tsv" />-->
+
+        <!--</test>-->
+    </tests>
+    <expand macro="citations" />
+    <help><![CDATA[
+=============================================================
+Spectral matching
+=============================================================
+-----------
+Description
+-----------
+
+Tool to perform spectral matching of MS/MS scans against library spectra
+
+The data inputs are:
+
+* library_db: An SQLite database of library ms/ms spectra (e.g. massbank, lipidsearch)
+* target_db: An SQLite database of the target ms/ms spectra (e.g. the data collected for an experiment)
+
+The library spectra can be downloaded from:
+
+* https://www.dropbox.com/s/csxj6pairsgd8fe/library_spectra.db?dl=1
+* (more official location) https://bioconductor.org/packages/release/data/experiment/src/contrib/msPurityData_1.6.0.tar.gz
+
+The target_db can be generated from the frag4feature galaxy tool but will accept any SQLite database in the same format.
+
+See Bioconductor documentation for more details, function msPurity::spectral_matching().
+
+-----------
+Outputs
+-----------
+If the 'create_new_db', a copy of the target_db will be created that will now including spectral matching results
+spectra. Otherwise the original SQLite database will be updpated
+
+* scan_hits: All spectral matching hits for every scan
+* xcms_hits: All spectral matching hits that can be linked to an XCMS grouped feature
+* sqlite_results (if create_new_db==True): SQLite database of all data including spectral matching results
+
+
+    ]]></help>
+</tool>
\ No newline at end of file