--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/frag4feature.xml	Mon Mar 05 09:58:58 2018 -0500
@@ -0,0 +1,141 @@
+<tool id="frag4feature" name="frag4feature" version="0.0.12">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements">
+        <!-- would ideally have xcms 3.0.0 but not available in bioconda at the point of tool creation-->
+        <requirement type="package" version="1.46.0" >bioconductor-xcms</requirement>
+    </expand>
+
+    <description>
+        Assign fragmentation spectra to XCMS features using msPurity
+    </description>
+ <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="Rscript"><![CDATA[
+        frag4feature.R
+            --out_dir=.
+            --xset=$xset
+            --pa=$pa
+            --cores=\${GALAXY_SLOTS:-4}
+            #if $file_load_conditional.file_load_select=="yes"
+                --mzML_files='
+                #for $i in $file_load_conditional.input
+                    $i,
+                #end for
+                '
+                --galaxy_names='
+                #for $i in $file_load_conditional.input
+                    $i.name,
+                #end for
+                '
+            #end if
+            --ppm=$ppm_f4f
+            --plim=$plim_f4f
+            #if $mostIntense_f4f
+                --mostIntense
+            #end if
+            #if $convert2RawRT_f4f
+                --convert2RawRT
+            #end if
+            #if $grp_peaklist_opt.grp_peaklist_opt=="yes"
+                --grp_peaklist=$grp_peaklist
+            #end if
+
+    ]]></command>
+    <inputs>
+
+        <param type="data" name="xset" label="xcmsSet object"
+               help="xcmsSet object saved as 'xset' in an RData file" format="rdata"/>
+        <param type="data" name="pa" label="purityA object" format="rdata"
+               help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/>
+
+        <param name="mostIntense_f4f" type="boolean" checked="true" label="For matching fragmentation to a feature,
+         use most intense peak within isolation window for precursor?"/>
+
+        <param name="convert2RawRT_f4f" type="boolean" checked="false" label="Was retention time correction used?"
+               help="If retention time correction has been used in XCMS set this to yes"/>
+
+        <param name="ppm_f4f" type="float" label="ppm" value="10"
+                    help="ppm tolerance between precursor mz and feature mz"/>
+
+        <param name="plim_f4f" type="float" label="plim" value="0" max="1" min="0"
+                    help="min purity of precursor to be included"/>
+
+        <conditional name="grp_peaklist_opt">
+            <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
+                <option value="yes" >Provide group peaklist </option>
+                <option value="no" selected="true">Use default grouped peaklist</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">
+                <param type="data" name="grp_peaklist" label="grouped peaklist"
+                    help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
+                          CAMERA annotations" format="tsv,tabular"/>
+            </when>
+        </conditional>
+
+        <expand macro="fileload" />
+
+    </inputs>
+    <outputs>
+	    <data name="frag4feature_grouped_msms" format="tsv" label="${tool.name} on ${on_string}: tsv"
+              from_work_dir="frag4feature.tsv" visible="true"/>
+        <data name="frag4feature_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
+              from_work_dir="frag4feature.RData" visible="true"/>
+        <data name="frag4feature_sqlite" format="sqlite" label="${tool.name} on ${on_string}: Sqlite"
+              from_work_dir="alldata.sqlite" visible="true"/>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="file_load_conditional">
+                <param name="file_load_select" value="yes"/>
+                <param name="input" >
+                    <collection type="list">
+                        <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
+                        <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
+                        <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
+                        <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
+                    </collection>
+                </param>
+            </conditional>
+            <param name="xset" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
+            <param name="pa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.assess_purity.rdata"/>
+            <output name="rag4feature_grouped_msms" value="frag4feature_output.tsv" >
+            </output>
+        </test>
+    </tests>
+    <expand macro="citations" />
+    <help><![CDATA[
+=============================================================
+Link fragmentation spectra to XCMS features
+=============================================================
+-----------
+Description
+-----------
+
+Tool to link XCMS features to fragmentation spectra and create an SQLite database of all the data and connections.
+
+The data inputs are:
+
+* A purityA object (generated from assess_purity_msms) saved in an rdata file.
+* A xcmsSet grouped object (generated from xcms_group) saved in an rdata file
+* [optional] a dataset collection of the mzML files to resubmit
+
+See Bioconductor documentation for more details, function msPurity::dimsPredictPurity()
+
+-----------
+Outputs
+-----------
+* frag4feature_rdata: An updated purityA object saved as rdata file with fragmentation-feature links added
+* frag4feature_grouped_msms: A flat file of all the XCMS peaks for each grouped feature and the corresponding fragmentation scans
+* frag4feature_sqlite: An SQLite database of the data (including fragmentation scans)
+
+
+
+    ]]></help>
+
+</tool>