annotate mfassignr_kmdnoise.xml @ 2:39a642fc9638 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit c6e502d8af84750003e4ba001c61817acedd1896

<tool id="mfassignr_kmdnoise" name="MFAssignR KMDNoise" version="@TOOL_VERSION@+galaxy0" profile="23.0">
    <description>Noise level assessment using the KMDNoise.</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_2940</edam_operation>    
    </edam_operations>
    <expand macro="creator" />
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript '${run_script}'
    ]]></command>
    <configfiles>
        <configfile name="run_script"><![CDATA[
        df <- read.delim("$input_file", sep="\t")
        names(df)[c(1,2)] <- c("mass", "intensity")
        assess_noise <- MFAssignR::KMDNoise(
            df = df,
            upper.y = $upper_y,
            lower.y = $lower_y,
            #if $upper_x
            upper.x = $upper_x,
            #end if
            #if $lower_x
            lower.x = $lower_x
            #end if
        )
        noise <- assess_noise[['Noise']]
        write.table(noise, file = '$Noise', row.names= FALSE, col.names = FALSE)
        ggplot2::ggsave(filename = "KMDplot.png", assess_noise[['KMD']])
        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="kmdnoise_param"/>
    </inputs>
    <outputs>
        <data name="Noise" format="txt" label="Noise level estimate by ${tool.name} on ${on_string}"/>
        <data name="KMD_plot" format="png" label="KMD plot by ${tool.name} on ${on_string}" from_work_dir="KMDplot.png"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="QC1_1_POS_500.tabular" />
            <output name="Noise" ftype="txt">
                <assert_contents>
                    <has_text text="3294705.63963789" />
                </assert_contents>
            </output>
            <output name="KMD_plot" ftype="png">
                <assert_contents>
                    <has_size size="1164615" delta="200"/>
                </assert_contents>
            </output>
        </test>    </tests>
    <help><![CDATA[
        @KMDNOISE_HELP@

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