view combineAnnotations.xml @ 6:ee5b9b2f529a draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit a1a069e7537aa4594974c74a08fb6e81e527203d

<tool id="mspurity_combineannotations" name="msPurity.combineAnnotations" version="0.2.2">
    <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"  optional="true"
               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"   optional="true"
               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"   optional="true"
               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>