view combineAnnotations.xml @ 3:b22aa0a9fc25 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty

<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
            #if $eic
                --eic
            #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."/>
       <param name="eic" type="boolean" label="Include EIC data?"
               help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
                     the database. Note, this will take considerable time for large datasets and
                     the resulting SQLite database can be large"/>
    </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>