Mercurial > repos > nml > biohansel_bionumeric_converter

<tool id="bionumeric_convert" name="biohansel2bionumerics" version="0.2.0">
    <description>compliant results</description>
    <requirements>
        <requirement type="package" version="0.24.1">pandas</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        $__tool_directory__/bionumeric_converter.py -f '$Input' -o '$Output'
    ]]></command>
    <inputs>
        <param type="data" name="Input" format="tabular"/>
    </inputs>
    <outputs>
        <data name="Output" format="csv" from_work_dir="output" label="Biohansel_Bionumerics"/>
    </outputs>
    <tests>
        <test>
            <param name="Input" value="results.tab"/>
            <output name="Output" value="Biohansel_Bionumerics.csv"/>
        </test>
    </tests>
    <help><![CDATA[
        **What it does**

        This tool is a supplementary script that takes Biohansel output data and converts it into a format compatible with Bionumerics.

        **Inputs:**

        - *Individual* output or *Collection* of outputs for any of the three Biohansel results files (tech_results.tab, match_results.tab, or results.tab)

        **Outputs:**

        - A .CSV file or a collection of .CSV files called "*Output*" that can be renamed and downloaded as required.

        **Specific modifications done to the data**

        1. Converts all commas in the output to "/"
        2. Splits Biohansel qc_message column into multiple columns if the message is longer than 150 characters
        3. Converts the .tab or .tsv file to a .csv file

    ]]></help>
    <citations>
    </citations>
</tool>
author	nml
date	Mon, 13 May 2019 12:59:15 -0400
parents	b000a3130db8
children