annotate recetox_aplcms_generate_feature_table.xml @ 0:2810c956ec39 draft

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

<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0">
    <description>generate feature table from noise-removed HRMS profile data</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[
             profile <- load_data_from_parquet_file('$profile')
             sample_name <- load_sample_name(profile)

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

             feature_table <- prof.to.features(
                 profile = profile,
                 bandwidth = $bandwidth,
                 #if $min_bandwidth:
                 min_bandwidth = $min_bandwidth,
                 #else:
                 min_bandwidth = NA,
                 #end if
                 #if $max_bandwidth:
                 max_bandwidth = $max_bandwidth,
                 #else:
                 max_bandwidth = NA,
                 #end if
                 sd_cut = c($sd_cut_min, $sd_cut_max),
                 #if $shape.shape_model == "bi-Gaussian":
                 sigma_ratio_lim = c($shape.sigma_ratio_lim_min, $shape.sigma_ratio_lim_max),
                 #else:
                 sigma_ratio_lim = NA,
                 #end if
                 shape_model = "$shape.shape_model",
                 peak_estim_method = "$peak_estim_method",
                 component_eliminate = $component_eliminate,
                 moment_power = $moment_power,
                 BIC_factor = $BIC_factor,
                 do.plot = FALSE
             )

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

    <inputs>
        <param label="Input profile data" name="profile" type="data" format="parquet"
               help="Mass spectrometry profile data." />
        <expand macro="bandwidth_params"/>
        <expand macro="generate_feature_table_params"/>
    </inputs>

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

    <tests>

    </tests>

    <help>
        <![CDATA[
            @GENERATE_FEATURE_TABLE_HELP@

            @GENERAL_HELP@
        ]]>
    </help>

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