diff combineAnnotations.xml @ 0:d6350a637d4a draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combineAnnotations.xml	Fri May 24 09:18:01 2019 -0400
@@ -0,0 +1,91 @@
+<tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="0.2.0">
+    <description>
+        Combine, score and rank metabolite annotation results
+    </description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements">
+    </expand>
+
+ <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="Rscript"><![CDATA[
+        combineAnnotations.R
+            --sm_resultPth="$sm_resultPth"
+            --metfrag_resultPth="$metfrag_resultPth"
+            --sirius_csi_resultPth="$sirius_csi_resultPth"
+            --probmetab_resultPth="$probmetab_resultPth"
+            --sm_weight=$sm_weight
+            --metfrag_weight=$metfrag_weight
+            --sirius_csi_weight=$sirius_csi_weight
+            --probmetab_weight=$probmetab_weight
+            #if $create_new_database:
+              --create_new_database
+            #end if
+
+    ]]></command>
+    <inputs>
+       <param name="sm_resultPth" type="data" label="Spectral matching result" format="sqlite"
+               help="The SQLite database generated from msPurity.spectralMatching"/>
+       <param name="metfrag_resultPth" type="data" label="Metfrag result" format="tsv,tabular"
+               help="The result of the MetFrag analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
+       <param name="sirius_csi_resultPth" type="data" label="Sirius CSI:FingerID result" format="tsv,tabular"
+               help="The result of the CSI:FingerID analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
+       <param name="probmetab_resultPth" type="data" label="Probmetab result" format="tsv,tabular"
+               help="The result of the Probmetab analysis (requires a column indicating the XCMS group ID and fragmentation spectra ID)"/>
+       <param name="sm_weight" type="float" min="0.0" max="1.0" value="0.4" label="Spectral matching weight" help="all weights need to sum to 1" />
+       <param name="metfrag_weight" type="float" min="0.0" max="1.0" value="0.25" label="Metfrag weight" help="all weights need to sum to 1" />
+       <param name="sirius_csi_weight" type="float" min="0.0" max="1.0" value="0.25" label="Sirius CSI:FingerID weight" help="all weights need to sum to 1" />
+       <param name="probmetab_weight" type="float" min="0.0" max="1.0" value="0.1" label="Probmetab weight" help="all weights need to sum to 1" />
+       <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 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."/>
+    </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="spectralMatching_db_with_spectral_matching.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" />
+            <output name="combined_annotations_tsv" file="combineAnnotations_combined_annotations.tsv" ftype="tsv" >
+            <assert_contents>
+                <has_n_columns n="32" />
+              </assert_contents>
+            </output>
+            <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>