+
−<tool id="recetox_aplcms_generate_feature_table" name="recetox-aplcms - generate feature table" version="@TOOL_VERSION@+galaxy0">
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−    <description>generate feature table from noise-removed HRMS profile data</description>
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−    <macros>
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−        <import>macros.xml</import>
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−        <import>help.xml</import>
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−    </macros>
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−    <expand macro="creator"/>
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−    <expand macro="requirements"/>
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−
+
−    <command detect_errors="aggressive"><![CDATA[
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−        Rscript -e 'source("${__tool_directory__}/utils.R")' -e 'source("${run_script}")'
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−    ]]></command>
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−    <configfiles>
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−         <configfile name="run_script"><![CDATA[
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−             profile <- load_data_from_parquet_file('$profile')
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−             sample_name <- load_sample_name(profile)
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−
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−             if(is.na(sample_name)) {
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−                 message("The file does not contain sample name.")
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−             }
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−
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−             feature_table <- prof.to.features(
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−                 profile = profile,
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−                 bandwidth = $bandwidth,
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−                 #if $min_bandwidth:
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−                 min_bandwidth = $min_bandwidth,
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−                 #else:
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−                 min_bandwidth = NA,
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−                 #end if
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−                 #if $max_bandwidth:
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−                 max_bandwidth = $max_bandwidth,
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−                 #else:
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−                 max_bandwidth = NA,
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−                 #end if
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−                 #if $advanced.sd_cut.sd_cut_bounds == "FALSE":
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−                 sd_cut = c($advanced.sd_cut.sd_cut_min, $advanced.sd_cut.sd_cut_max),
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−                 #else
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−                 sd_cut = c(0, Inf),
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−                 #end if
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−                 sigma_ratio_lim = determine_sigma_ratios($advanced.shape_model.sigma_ratio_lim_min, $advanced.shape_model.sigma_ratio_lim_max),
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−                 shape_model = "bi-Gaussian",
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−                 peak_estim_method = "$advanced.peak_estim.peak_estim_method",
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−                 component_eliminate = $advanced.component_eliminate,
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−                 #if $advanced.peak_estim.peak_estim_method == "moment":
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−                 moment_power = $advanced.peak_estim.moment_power,
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−                 #else
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−                 moment_power = 1,
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−                 #end if
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−                 BIC_factor = $BIC_factor,
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−                 do.plot = FALSE
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−             )
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−
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−             feature_table <- save_sample_name(feature_table, sample_name)
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−             save_data_as_parquet_file(feature_table, '$output_file')
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−         ]]></configfile>
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−    </configfiles>
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−
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−    <inputs>
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−        <param label="Input profile data" name="profile" type="data" format="parquet"
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−               help="Mass spectrometry profile data." />
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−        <expand macro="bandwidth_params"/>
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−        <expand macro="generate_feature_table_params"/>
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−    </inputs>
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−
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−    <outputs>
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−        <data label="${tool.name} on ${on_string}" name="output_file" format="parquet" />
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−    </outputs>
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−
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−    <tests>
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−
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−    </tests>
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−
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−    <help>
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−        <![CDATA[
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−            @GENERATE_FEATURE_TABLE_HELP@
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−
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−            @GENERAL_HELP@
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−        ]]>
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−    </help>
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−
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−    <expand macro="citations"/>
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−</tool>