--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filterFragSpectra.xml	Thu Mar 04 12:15:17 2021 +0000
@@ -0,0 +1,99 @@
+<tool id="mspurity_filterfragspectra" name="msPurity.filterFragSpectra" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+    <description>
+      Filter fragmentations spectra associated with an XCMS feature
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code" interpreter="Rscript"><![CDATA[
+        filterFragSpectra.R
+            --out_rdata='$filterFragSpectra_output_rdata'
+            --out_peaklist_prec='$filterFragSpectra_output_prec_tsv'
+            --out_peaklist_frag='$filterFragSpectra_output_frag_tsv'
+            --pa='$pa'
+            --ilim=$ilim
+            --plim=$plim
+            --ra=$ra
+            --snr=$snr
+            --snmeth=$snmeth
+            $rmp
+    ]]></command>
+    <inputs>
+        <param argument="--pa" type="data"
+               label="purityA object with fragmentation linked to XCMS features" format="rdata"
+               help="purityA object saved as 'pa' in a RData file where fragmentation has
+                     been linked to XCMS features(output from frag4feature tool)"/>
+        <param argument="--plim" type="float" value="0.5" help=""
+               label="Miniumum precursor ion purity of the associated precursor for
+                     fragmentation spectra scan"  />
+        <param argument="--ilim" type="float" value="0.0" label="Peak instensity threshold" help="" />
+        <param argument="--ra" type="float" min="0.0" max="1.0" value="0.0"
+               label="Relative abundance threshold" help="" />
+        <param argument="--snr" type="float" value="0.0" label="Signal-to-noise threshold" help="" />
+        <param argument="--snmeth" type="select" label="Function to calculate noise." help="" >
+            <option value="median" selected="true">median</option>
+            <option value="mean">mean</option>
+            <!-- <option value="mad">mad</option> -->
+        </param>
+        <param argument="--rmp" type="boolean" checked="false" truevalue="--rmp" falsevalue=""
+               label="Remove peaks that do not meet the filtering criteria.
+                      Otherwise peaks will be flagged instead."
+               help="" />
+    </inputs>
+    <outputs>
+        <data name="filterFragSpectra_output_rdata" format="rdata"
+              label="${tool.name} on ${on_string}: RData" />
+        <data name="filterFragSpectra_output_prec_tsv" format="tsv"
+              label="${tool.name} on ${on_string}: peaklist (precursors)" />
+        <data name="filterFragSpectra_output_frag_tsv" format="tsv"
+              label="${tool.name} on ${on_string}: peaklist (fragments)" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="pa" value="frag4feature_output.RData" />
+            <output name="filterFragSpectra_output_rdata"
+                    file="filterFragSpectra_output.RData" ftype="rdata" compare="sim_size" />
+            <output name="filterFragSpectra_output_prec_tsv"
+                    file="filterFragSpectra_output_prec.tsv" ftype="tsv" />
+            <output name="filterFragSpectra_output_frag_tsv"
+                    file="filterFragSpectra_output_frag.tsv" ftype="tsv" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+=============================================================
+Filter Fragmentation Spectra
+=============================================================
+-----------
+Description
+-----------
+
+Flag and filter features based on signal-to-noise ratio, relative abundance, intensity threshold and precursor ion purity of precursor.
+
+
+**Example LC-MS/MS processing workflow**
+
+
+* Purity assessments
+    +  (mzML files) -> purityA -> (pa)
+* XCMS processing
+    +  (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
+* Fragmentation processing
+    + (xset, pa) -> frag4feature -> **filterFragSpectra** -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)
+
+See Bioconductor documentation for more details, functions:
+msPurity::filterFragSpectra()
+
+-----------
+Outputs
+-----------
+* filter_fragmentation_spectra_rdata: RData of the purityA object (pa) with filtered data
+* peaklist_prec_tsv: precursor peaklist
+* peaklist_frag_tsv: fragmentation peaklist
+
+    ]]></help>
+
+    <expand macro="citations" />
+
+</tool>