annotate mfassignr_findRecalSeries.xml @ 1:ad4176b336dc draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit c16561e825cd376dec5f5c252dc8743ad1dc2ca4

<tool id="mfassignr_findRecalSeries" name="MFAssignR FindRecalSeries" version="@TOOL_VERSION@+galaxy1" profile="23.0">
    <description>Selects most suitable series for recalibration</description>
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>
    <edam_topics>
        <edam_topic>topic_3172</edam_topic>    
    </edam_topics>
    <edam_operations>  
        <edam_operation>operation_3627</edam_operation>  
    </edam_operations>
    <expand macro="creator" />
    <expand macro="refs" />

    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript -e 'packageVersion("MFAssignR")' &&
        Rscript '${mfassignr_findrecalseries}'
    ]]>
    </command>
    <configfiles>
        <configfile name="mfassignr_findrecalseries"><![CDATA[
            library(dplyr)
            df <- read.table("$input_file", header=TRUE, sep="\t")
            result <- MFAssignR::FindRecalSeries(
                df = df,
                global_min = $global_min,
                global_max = $global_max,
                number_of_combinations = $number_of_combinations,
                abundance_score_threshold = $abundance_score_threshold,
                peak_distance_threshold = $peak_distance_threshold,
                coverage_threshold = $coverage_threshold,
                fill_series = $fill_series
            ) |> dplyr::rename(Series = series)
            
            write.table(result, file="$final_series", sep="\t", row.names=FALSE)
        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="findrecalseries_param"/>
    </inputs>
    <outputs>
        <data name="final_series" format="tabular" label="Final recalibration series"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="recallist/recal_series.tabular"/>
            <param name="global_min" value="100"/>
            <param name="global_max" value="500"/>
            <param name="abundance_score_threshold" value="50"/>
            <param name="number_of_combinations" value="3"/>
            <param name="coverage_threshold" value="50"/>
            <param name="fill_series" value="TRUE"/>
            <output name="final_series" file="findrecalseries/selected_series.tabular"/>
        </test>
    </tests>
    <help>
        @FINDRECALSERIES_HELP@

        @GENERAL_HELP@
    </help>
    <expand macro="citations"/>
</tool>