comparison spamr_vet_tools_v2/quast_get_fasta.xml @ 2:d7b099fbb003 draft default tip

Corrected file names and updated tool wrappers for consistency.

2:d7b099fbb003

<tool id="quast_get_fasta"
      name="QUAST Analysis and FASTA Generator"
      version="0.1.0+galaxy0"
      profile="21.05">

    <description>Extracts QUAST metrics and generates FASTA files from JSON input.</description>

    <requirements>
        <requirement type="package" version="3.12">python</requirement>
    </requirements>

    <command detect_errors="exit_code">
        <![CDATA[
        python '$__tool_directory__/quast_get_fasta.py' '$json_input'
        ]]>
    </command>

    <inputs>
        <param name="json_input" type="data" format="json" label="Input JSON File"
               help="Provide a JSON file containing QUAST and Shovill results."/>
    </inputs>

    <outputs>
        <data name="csv_output" format="csv" from_work_dir="quast_output.csv"
              label="QUAST Summary on ${on_string}"/>
        <data name="fasta_output" format="fasta" from_work_dir="shovill_contigs.fasta"
              label="Shovill Contigs on ${on_string}"/>
    </outputs>

    <tests>
        <test>
            <param name="json_input" value="example_input.json"/>
            <output name="csv_output" file="expected_output.csv" compare="diff"/>
            <output name="fasta_output" file="expected_output.fasta" compare="diff"/>
        </test>
    </tests>

    <help><![CDATA[
QUAST Analysis and FASTA Generator
==================================

This tool extracts key statistics from **QUAST** and generates a **FASTA** file containing assembled contigs from **Shovill**.

Usage Instructions
------------------
1. Upload or provide a **JSON file** containing **QUAST** and **Shovill** results.
2. The tool will:
   - Extract **assembly metrics** from QUAST and save them as a CSV.
   - Convert **contigs from Shovill** into a FASTA file.
3. The outputs will be:
   - `quast_output.csv` (QUAST summary metrics)
   - `shovill_contigs.fasta` (FASTA file with contigs)

Outputs
-------
- **CSV File:** Contains QUAST summary metrics such as `N50`, `GC content`, `total length`, `L50`, and other key assembly statistics.
- **FASTA File:** Extracts contigs from **Shovill**, formatting them properly for downstream analysis.

References
----------
- `QUAST <http://bioinf.spbau.ru/quast>`_ - Quality assessment tool for genome assemblies.
- `Shovill <https://github.com/tseemann/shovill>`_ - A tool for rapid bacterial genome assembly using SPAdes.

For questions or issues, please contact the tool maintainers.
    ]]></help>

</tool>