view tooldistillator_summarize.xml @ 11:f4f71128f097 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator commit 5afafa93bbb331db2e3f2e700714ff60bf467b27

<tool id="tooldistillator_summarize" name="ToolDistillator Summarize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Aggregate several JSON reports from ToolDistillator
    </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
tooldistillator --version &&
mkdir -p input_files &&
#for $file in $summarize_data
cp '$file' ./input_files/ &&
#end for
tooldistillator 
    summarize
    input_files/*
    -o summary.json
]]>
    </command>
    <inputs>
        <param name="summarize_data" type="data" multiple="true" format="json" label="Results in Json format" help="Summarize results from tooldistillator in json format"/>
    </inputs>
    <outputs>
        <data name="summary_json" format="json" from_work_dir="summary.json" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1"> <!-- TEST_1 sumarize json results -->
            <param name="summarize_data" ftype="json" value="summarize/abricate_output.json,summarize/bracken_full_output.json,summarize/plasmidfinder_output.json"/>
            <output name="summary_json" ftype="json" value="summarize/summarize.json" compare="sim_size">
                <assert_contents>
                    <has_text_matching expression="Enterococcus.*faecalis" />
                    <has_json_property_with_text property="name" text="plasmid_hit" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.



This tool here summarize JSON output file from ToolDistillator to only one JSON file
    ]]></help>
    <expand macro="citations"/>
</tool>