<commit_before><tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy" version="@WRAPPER_VERSION@.0">
    <description>summaries and plots</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>summarize_taxa_through_plots.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        summarize_taxa_through_plots.py
            -i '$otu_table_fp'
            -o summarize_taxa_through_plots
            #if $mapping_fp
                -m '$mapping_fp'
            #end if
            #if $mapping_category
                -c '$mapping_category'
            #end if
            '$sort'
        && mkdir -p $area_charts_html_report.files_path
        && cp -r summarize_taxa_through_plots/taxa_summary_plots/area_charts.html '$area_charts_html_report.files_path'
        && cp -r summarize_taxa_through_plots/taxa_summary_plots/charts '$area_charts_html_report.files_path'
        && cp -r summarize_taxa_through_plots/taxa_summary_plots/css '$area_charts_html_report.files_path'
        && cp -r summarize_taxa_through_plots/taxa_summary_plots/js '$area_charts_html_report.files_path'
        && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report'

        && mkdir -p $bar_charts_html_report.files_path
        && cp -r summarize_taxa_through_plots/taxa_summary_plots/bar_charts.html '$bar_charts_html_report.files_path'
        && cp -r summarize_taxa_through_plots/taxa_summary_plots/charts '$bar_charts_html_report.files_path'
        && cp -r summarize_taxa_through_plots/taxa_summary_plots/css '$bar_charts_html_report.files_path'
        && cp -r summarize_taxa_through_plots/taxa_summary_plots/js '$bar_charts_html_report.files_path'
        && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report'
    ]]></command>
    <inputs>
        <param name="otu_table_fp" type="data" format="biom,tabular,txt" label="Input OTU table" help="(-i/--otu_table_fp)"/>
        <param name="mapping_fp" type="data" format="tabular,csv" label="Input metadata mapping (optional)" help="(-m, --mapping_fp)" optional="True"/>
        <param name="mapping_category" type="text" value="" label="Category to use to summarize OTU table"  help="(-c/--mapping_category)" optional="True"/>
        <param name="sort" type="boolean" label="Sort OTU table?" truevalue="--sort" falsevalue="" selected="False" help="(-s/--sort)"/>
    </inputs>
    <outputs>
        <data name="L2_tab" format="tabular"  from_work_dir="summarize_taxa_through_plots/*_L2.txt" label="${tool.name} on ${on_string}: L2 tab">
            <filter>"2" in level and suppress_classic_table_output is False</filter>
        </data>
        <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa_through_plots/*_L3.txt" label="${tool.name} on ${on_string}: L3 tab">
            <filter>"3" in level and suppress_classic_table_output is False</filter>
        </data>
        <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa_through_plots/*_L4.txt" label="${tool.name} on ${on_string}: L4 tab">
            <filter>"4" in level and suppress_classic_table_output is False</filter>
        </data>
        <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa_through_plots/*_L5.txt" label="${tool.name} on ${on_string}: L5 tab">
            <filter>"5" in level and suppress_classic_table_output is False</filter>
        </data>
        <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa_through_plots/*_L6.txt" label="${tool.name} on ${on_string}: L6 tab">
            <filter>"6" in level and suppress_classic_table_output is False</filter>
        </data>
        <data name="bar_charts_html_report" format="html" label="${tool.name} on ${on_string}: Bar charts">
            <filter>'bar' is chart_type</filter>
        </data>
        <data name="area_charts_html_report" format="html" label="${tool.name} on ${on_string}: Area charts">
            <filter>'area' is chart_type</filter>
        </data>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help><![CDATA[
**What it does**
<commit_msg>Clean summarize_taxa_through_plots<commit_after><tool id="qiime_summarize_taxa_through_plots" name="Perform taxonomy" version="@WRAPPER_VERSION@.0">
    <description>summaries and plots</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>summarize_taxa_through_plots.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        summarize_taxa_through_plots.py
            --otu_table_fp '$otu_table_fp'
            --output_dir output
            #if $parameter_fp
                --parameter_fp '$parameter_fp'
            #end if
            #if $mapping.use_mapping == "yes"
                --mapping_fp '$mapping.mapping_fp'
                #if str($mapping.mapping_category) != ''
                    --mapping_category '$mapping.mapping_category'
                #end if
            #end if
            $sort
        && mkdir -p '$area_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/area_charts.html' '$area_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/charts' '$area_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/css' '$area_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/js' '$area_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/raw_data' '$area_charts_html_report.files_path'
        && mv '$area_charts_html_report.files_path/area_charts.html' '$area_charts_html_report'

        && mkdir -p '$bar_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/bar_charts.html' '$bar_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/charts' '$bar_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/css' '$bar_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/js' '$bar_charts_html_report.files_path'
        && cp -r 'output/taxa_summary_plots/raw_data' '$bar_charts_html_report.files_path'
        && mv '$bar_charts_html_report.files_path/bar_charts.html' '$bar_charts_html_report'
    ]]></command>
    <inputs>
        <param argument="--otu_table_fp" type="data" format="biom,tabular,txt" label="Input OTU table"/>
        <conditional name="mapping">
            <param name="use_mapping" type="select" label="Use a metadata mapping file?">
                <option value="yes">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes">
                <param argument="--mapping_fp" type="data" format="tabular,csv" label="Input metadata mapping"/>
                <param argument="--mapping_category" type="text" value="" label="Category to use to summarize OTU table" optional="True"/>
            </when>
            <when value="no"/>
        </conditional>
        <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior of join_paired_ends.py" optional="true"/>
        <param argument="--sort" type="boolean" label="Sort OTU table?" truevalue="--sort" falsevalue="" checked="False"/>
    </inputs>
    <outputs>
        <collection name="otu_table" type="list" label="${tool.name} on ${on_string}: OTU tables for the different taxonomic levels">
            <discover_datasets pattern=".*_L(?P&lt;designation&gt;.+)\.txt" directory="output/" />
        </collection>
        <collection name="biom_otu_table" type="list" label="${tool.name} on ${on_string}: BIOM OTU tables for the different taxonomic levels">
            <discover_datasets pattern=".*_L(?P&lt;designation&gt;.+)\.biom" format="biom1" directory="output/" />
        </collection>
        <data name="bar_charts_html_report" format="html" label="${tool.name} on ${on_string}: Bar charts"/>
        <data name="area_charts_html_report" format="html" label="${tool.name} on ${on_string}: Area charts"/>
    </outputs>
    <tests>
        <test>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

{'fraction_non_alphanumeric': 0.1388050694025347, 'fraction_numerical': 0.002776101388050694, 'mean_word_length': 3.395755968169761, 'pattern_counts': {'":': 0, '<': 105, '<?xml version=': 0, '>': 103, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3104948', 'n_tokens_mistral': 2748, 'n_tokens_neox': 2608, 'n_words': 475}