annotate mfassignr_recallist.xml @ 5:4f671baab2fd draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 1e98df2131b9b5384ca2e4310f93270eae6f517c

<tool id="mfassignr_recallist" name="MFAssignR RecalList" version="@TOOL_VERSION@+galaxy0" profile="23.0">
    <description>Identification of candidate 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="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript '${run_script}'
    ]]></command>
    <configfiles>
        <configfile name="run_script"><![CDATA[
            df <- read.delim("$input_file", sep="\t")
            recal <- MFAssignR::RecalList(
                df = df
            )

            write.table(recal, file = '$recal_series', row.names= FALSE, sep = "\t")
        ]]></configfile>
    </configfiles>
    <inputs>
        <param name="input_file" type="data" format="tabular" label="Input data"
               help= "Input data frame - output from MFAssign or MFAssignCHO. Recommended are 'Unambiguous' assignments."/>
    </inputs>
    <outputs>
        <data name="recal_series" format="tabular" label="Recalibration series by ${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
         <test>
            <param name="input_file" value="mfassigncho/unambig.tabular" />
            <output name="recal_series" file="recallist/recal_series.tabular" lines_diff="100"/>
        </test>
    </tests>
    <help><![CDATA[
        @RECALLIST_HELP@

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