annotate recetox_aplcms_correct_time.xml @ 0:4d7db9cdd952 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 506df2aef355b3791567283e1a175914f06b405a

<tool id="recetox_aplcms_correct_time" name="recetox-aplcms - correct time" version="@TOOL_VERSION@+galaxy0">
    <description>correct retention time across samples for peak alignment</description>
    <macros>
        <import>macros.xml</import>
        <import>help.xml</import>
    </macros>
    <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[
              features_table <- load_data_from_parquet_file('$features_table')
              sample_name <- load_sample_name(features_table)

              if(is.na(sample_name)) {
                  message("The file does not contain sample name.")
              }

              template_features <- load_data_from_parquet_file('$template')
              tolerances <- load_data_from_parquet_file('$tolerances')

              corrected_table <- correct_time(
                   this.feature = features_table,
                   template_features = template_features,
                   mz_tol_relative = get_mz_tol(tolerances),
                   rt_tol_relative = get_rt_tol(tolerances)
              )

              corrected_table <- save_sample_name(corrected_table, sample_name)
              save_data_as_parquet_file(corrected_table, '$output_file')
         ]]></configfile>
    </configfiles>

    <inputs>
        <param label="Input clustered features table" name="features_table" type="data" format="parquet"
               help="Mass spectrometry clustered features table." />
        <param label="Input template features table" name="template" type="data" format="parquet"
               help="Template features table." />
        <param label="Input tolerances values" name="tolerances" type="data" format="parquet"
               help="Table containing tolerance values." />
    </inputs>

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

    <tests>

    </tests>

    <help>
        <![CDATA[
            @CORRECT_TIME_HELP@

            @GENERAL_HELP@

            @EXAMPLE_OUTPUT@
        ]]>
    </help>

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