--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combineAnnotations.xml	Wed Nov 27 13:51:34 2019 -0500
@@ -0,0 +1,128 @@
+<tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+    <description>Combine, score and rank metabolite annotation results</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/combineAnnotations.R'
+            --sm_resultPth='$sm_resultPth'
+            --metfrag_resultPth='$metfrag_resultPth'
+            --sirius_csi_resultPth='$sirius_csi_resultPth'
+            --probmetab_resultPth='$probmetab_resultPth'
+            --ms1_lookup_resultPth='$ms1_lookup_resultPth'
+
+            #if $ms1_lookup_checkAdducts:
+              --ms1_lookup_checkAdducts
+            #end if
+
+            --ms1_lookup_keepAdducts='$ms1_lookup_keepAdducts'
+            --ms1_lookup_dbSource=$ms1_lookup_dbSource
+
+            --sm_weight=$sm_weight
+            --metfrag_weight=$metfrag_weight
+            --sirius_csi_weight=$sirius_csi_weight
+            --probmetab_weight=$probmetab_weight
+            --ms1_lookup_weight=$ms1_lookup_weight
+            --biosim_weight=$biosim_weight
+
+
+            #if $create_new_database:
+              --create_new_database
+            #end if
+
+            --compoundDbType=$compoundDbTypeCond.compoundDbType
+
+            #if $compoundDbTypeCond.compoundDbType== 'sqlite'
+              --compoundDbPth='$compoundDbTypeCond.compoundDbPth'
+            #end if
+
+
+    ]]></command>
+    <inputs>
+
+
+      <param argument="--sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
+               help="The SQLite database generated from msPurity.spectralMatching"/>
+      <param argument="--metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular"  optional="true"
+               help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID)"/>
+      <param argument="--sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular"   optional="true"
+             help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID)"/>
+      <param argument="--probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular"   optional="true"
+               help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID)"/>
+      <param argument="--ms1_lookup_resultPth" type="data" label="MS1 Lookup result" format="tsv,tabular"   optional="true"
+             help="The result of the a generic MS1 lookup annotation software (e.g. BEAMS can be used)"/>
+      <param argument="--ms1_lookup_keepAdducts" type="text" label="MS1 lookup adducts to keep" optional="true"
+             help="Provide a list of adducts that should be used from the MS1 lookup (e.g. [M+H]+, [M+Na]+"/>
+      <param argument="--ms1_lookup_checkAdducts" type="boolean" label="MS1 lookup check adducts to CAMERA"
+             help="Check if adducts match to those found in CAMERA (requires the database to have been created with CAMERA object"/>
+      <param argument="--ms1_lookup_dbSource" type="select" label="MS1 lookup database source" help="Which database was used for the MS1 lookup" >
+                <option value="hmdb" selected="true">hmdb</option>
+                <option value="pubchem">pubchem</option>
+                <option value="kegg">kegg</option>
+      </param>
+      <param argument="--sm_weight" type="float" min="0.0" max="1.0" value="0.3" label="Spectral matching weight" help="all weights need to sum to 1" />
+      <param argument="--metfrag_weight" type="float" min="0.0" max="1.0" value="0.2" label="Metfrag weight" help="all weights need to sum to 1" />
+      <param argument="--sirius_csi_weight" type="float" min="0.0" max="1.0" value="0.2" label="Sirius CSI:FingerID weight" help="all weights need to sum to 1" />
+      <param argument="--probmetab_weight" type="float" min="0.0" max="1.0" value="0.0" label="Probmetab weight" help="all weights need to sum to 1" />
+      <param argument="--ms1_lookup_weight" type="float" min="0.0" max="1.0" value="0.05" label="MS1 Lookup weight" help="all weights need to sum to 1" />
+      <param argument="--biosim_weight" type="float" min="0.0" max="1.0" value="0.25" label="Biological similarity weight" help="all weights need to sum to 1" />
+      <param argument="--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 spectral matching database and the results will be added to this copy.
+                     When False, the input SQLite database will be updated the results. Use False
+                     if you want to reduce storage space being used."/>
+
+      <conditional name="compoundDbTypeCond">
+            <param argument="--compoundDbType" type="select" label="compoundDbType" help="Database type for compound database to be used full database available on request - contact t.n.lawson@bham.ac.uk)." >
+                <option value="sqlite" selected="true">SQLite</option>
+                <option value="local_config"  >Locally configured MySQL, Postgres or SQLite database</option>
+            </param>
+            <when value="sqlite">
+               <param argument="--compoundDbPth" type="data" label="SQLite compound database pth" format="sqlite" help=""/>
+            </when>
+            <when value="local_config">
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="combined_annotations_sqlite" from_work_dir="combined_annotations.sqlite" format="sqlite" label="${tool.name} on ${on_string}: sqlite" />
+        <data name="combined_annotations_tsv" from_work_dir="combined_annotations.tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="sm_resultPth" value="combinedAnnotation_input_spectralMatching.sqlite" />
+            <param name="metfrag_resultPth" value="combineAnnotations_input_metfrag.tsv" />
+            <param name="sirius_csi_resultPth" value="combineAnnotations_input_sirus_csifingerid.tsv" />
+            <param name="probmetab_resultPth" value="combineAnnotations_input_probmetab.tsv" />
+            <param name="beams_resultPth" value="combineAnnotations_input_beams.tsv" />
+            <param name="compoundDbTypeCond|compoundDbPth" value="metab_compound_subset.sqlite" />
+            <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" />
+            <output name="combined_annotations_sqlite" file="combineAnnotations_combined_annotations.sqlite" ftype="sqlite" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+=============================================================
+Combine annotation results
+=============================================================
+-----------
+Description
+-----------
+
+Tool to combine the annotation results from msPurity spectral matching, MetFrag, Sirius CSI:FingerID and probmetab
+based on weighted scores for each technique aligning each annotation by inchikey and XCMS grouped feature.
+
+See Bioconductor documentation for more details, functions:
+msPurity::combineAnnotation()
+
+-----------
+Outputs
+-----------
+* combined_annotation_sqlite
+* combined_annotation_tsv
+
+    ]]></help>
+
+<expand macro="citations" />
+
+</tool>