annotate mfassignr_recal.xml @ 6:cfcf45ba58be draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 7d98b78ae27b24ee581d40ff0b624d7ecb288030

<tool id="mfassignr_recal" name="MFAssignR Recal" version="@TOOL_VERSION@+galaxy0" profile="23.0">
    <description>Internal mass recalibration using a recalibrant series.</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="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript '${run_script}'
    ]]></command>
    <configfiles>
        <configfile name="run_script"><![CDATA[
            df <- read.delim("$input_file", sep="\t")
            peaks <- read.delim("$peaks", sep="\t")
            SN <- $sn_ratio * $kmdn

            series <- read.delim('$series', sep='\t')

            recal <- MFAssignR::Recal(
                df = df,
                peaks = peaks,
                #if $isopeaks
                isopeaks = read.delim("$isopeaks", sep="\t"),
                #end if
                mode = "$ionmode",
                SN = SN,
                mzRange = $mzRange,
                step_O = $step_O,
                step_H2 = $step_H2,
                CalPeak = $CalPeak,
                series1 = series[1, "Series"],
                series2 = series[2, "Series"],
                series3 = series[3, "Series"],
                series4 = series[4, "Series"],
                series5 = series[5, "Series"],
                series6 = series[6, "Series"],
                series7 = series[7, "Series"],
                series8 = series[8, "Series"],
                series9 = series[9, "Series"],
                series10 = series[10, "Series"]
            )

            write.table(recal[['Mono']], file = '$Mono', row.names= FALSE, sep="\t")
            write.table(recal[['Iso']], file = '$Iso', row.names= FALSE, sep="\t")
            write.table(recal[['RecalList']], file = '$Recalibrants', row.names= FALSE, sep="\t")
            ggplot2::ggsave(filename = "MZplot.png", recal[['Plot']])

        ]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="recal_param"/>
    </inputs>
    <outputs>
        <data name="Mono" format="tabular" label="Recalibrated 'Mono' list by ${tool.name} on ${on_string}"/>
        <data name="Iso" format="tabular" label="Recalibrated 'Iso' list by ${tool.name} on ${on_string}"/>
        <data name="Recalibrants" format="tabular" label="Recalibrants list (RecalOut) by ${tool.name} on ${on_string}"/>
        <data name="MZplot" format="png" label="MZ plot by ${tool.name} on ${on_string}" from_work_dir="MZplot.png"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="mfassigncho/unambig.tabular"/>
            <param name="series" value="recallist/recal_series.tabular"/>
            <param name="peaks" value="isofiltr/mono_out.tabular"/>              
            <param name="isopeaks" value="isofiltr/iso_out.tabular"/>
            <output name="Mono">
                <assert_contents>
                    <has_n_lines n="9156"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output name="Iso">
                <assert_contents>
                    <has_n_lines n="2521"/>
                    <has_n_columns n="4"/>
                </assert_contents>
            </output>
            <output name="Recalibrants" file="recal/recalibrants.tabular"/>
            <output name="MZplot">
                <assert_contents>
                    <has_size size="91080" delta="200"/>
                </assert_contents>
            </output> 
        </test> 
    </tests>
    <help><![CDATA[
        @RECAL_HELP@

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