comparison XSeekerPreparator.xml @ 4:8cc9fc8eacac draft

" master branch Updating"

3:fa97d16330be

        <edam_operation>operation_1812</edam_operation>
        <edam_operation>operation_0335</edam_operation>
    </edam_operations>
    
    <requirements>
        <requirement type="set_environment">R_SCRIPT</requirement>
        <requirement type="package" version="4.0.0">R</requirement>
        <requirement type="package" version="1.6.6">optparse</requirement>
        <requirement type="package" version="3.10.2">xcms</requirement>
        <requirement type="package" version="1.2.1">blob</requirement>
        <requirement type="package" version="0.9.4">fst</requirement>
        <requirement type="package" version="1.4.0">stringr</requirement>
        <requirement type="package">DBModelR</requirement>
    </requirements>
    
    <stdio>

        <exit_code 
            range="1"
            level="warning"

        />

    </stdio>

    <version_command>
        $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R' -v
    </version_command>

    <command>
        <![CDATA[
            $R_SCRIPT '$__tool_directory__/XSeekerPreparator.R'

                -P

                --input '$input'
                --output '$output'

                #if $samples.selected
                    --samples '${",".join(samples.selected)}'
                #end if

                #if $database.archetypes
                    --archetype '${",".join($database.archetypes)}'
                #end if

    </inputs>


    <outputs>
        <data format="sqlite" name="output" />
    </outputs>

    <configfiles>
        <configfile name="base_config">
tryCatch({

4:8cc9fc8eacac

        <edam_operation>operation_1812</edam_operation>
        <edam_operation>operation_0335</edam_operation>
    </edam_operations>
    
    <requirements>
        <requirement type="package" version="3.12.0">bioconductor-xcms</requirement>
        <requirement type="package">bioconductor-camera</requirement>
        <requirement type="package" version="2.29.2">git</requirement> 
        <requirement type="package" version="4.0">R</requirement>
        <requirement type="package" version="1.2.1">r-blob</requirement>
        <requirement type="package" version="1.1.0">r-dbi</requirement>
        <requirement type="package" version="0.9.4">r-fst</requirement>
        <requirement type="package" version="1.6.6">r-optparse</requirement>
        <requirement type="package" version="1.4.0">r-stringr</requirement>
        <requirement type="package" version="0.3.4">r-purrr</requirement>
        <requirement type="package" version="2.2.1">r-rsqlite</requirement>
        <requirement type="package" version="0.1.0">r-dbmodelr</requirement>
    </requirements>
    <stdio>

        <exit_code 
            range="1"
            level="warning"

        />

    </stdio>

    <version_command>
        Rscript '$__tool_directory__/XSeekerPreparator.R' -v
    </version_command>

    <command>
        <![CDATA[
            Rscript '$__tool_directory__/XSeekerPreparator.R'

                -P

                --input '$input'
                --output '$output'

                #if $samples.selected
                    --samples '${",".join($samples.selected)}'
                #end if

                #if $database.archetypes
                    --archetype '${",".join($database.archetypes)}'
                #end if

    </inputs>


    <outputs>
        <data format="sqlite" name="output" />
        <!-- <data format="xseeker.sqlite" name="output" /> -->
    </outputs>

    <configfiles>
        <configfile name="base_config">
tryCatch({