annotate recetox_aplcms_compute_template.xml @ 8:4963811b6dec draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit bc3445f7c41271b0062c7674108f57708d08dd28

<tool id="recetox_aplcms_compute_template" name="recetox-aplcms - compute template" version="@TOOL_VERSION@+galaxy2" profile="21.09">
    <description>compute retention time correction template feature table</description>
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>
    <expand macro="annotation"/>
    <edam_operations>
        <edam_operation>operation_3936</edam_operation>
    </edam_operations>
    <expand macro="refs"/>
    <expand macro="creator"/>
    <expand macro="requirements"/>

    <command detect_errors="aggressive"><![CDATA[
        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
    ]]></command>
    <configfiles>
         <configfile name="run_script"><![CDATA[
              #set filenames = str("', '").join([str($f) for $f in $files])
              feature_tables <- load_parquet_collection(c('$filenames'))

              template_features <- compute_template(feature_tables)

              save_data_as_parquet_file(template_features, '$output_file')
         ]]></configfile>
    </configfiles>

    <inputs>
        <param name="files" type="data_collection" collection_type="list" format="parquet" label="Input data"
               help="Table containing clustered features." />
    </inputs>

    <outputs>
        <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" />
    </outputs>

    <tests>
        <test expect_failure="true" />
    </tests>
    
    <help>
        <![CDATA[
            @COMPUTE_TEMPLATE_HELP@

            @GENERAL_HELP@
            
        ]]>
    </help>

    <expand macro="citations"/>
</tool>