view DownloadSchema.xml @ 1:4683f2baa5f0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751

<tool id="chewbbaca_downloadschema" name="chewBBACA DownloadSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Download a schema from Chewie-NS</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        chewBBACA.py DownloadSchema
            -sp $species_id 
            -sc $schema_id
            -o 'output' &&
        ## The output is named based on the species name. Rename it to schema_seed so it is compatible for other chewbbaca tools.
        mv output/* 'schema_seed' &&
        zip -r schema_seed.zip 'schema_seed'
    ]]></command>
    <inputs>
        <param argument="--species-id" type="select" label="Species ID">
            <option value="1">Streptococcus pyogenes</option>
            <option value="2">Acinetobacter baumannii</option>
            <option value="3">Arcobacter butzleri</option>
            <option value="4">Campylobacter jejuni</option>
            <option value="5">Escherichia coli</option>
            <option value="6">Listeria monocytogenes</option>
            <option value="7">Yersinia enterocolitica</option>
            <option value="8">Salmonella enterica</option>
            <option value="9">Streptococcus agalactiae</option>
            <option value="10">Brucella melitensis</option>
            <option value="11">Brucella</option>
            <option value="12">Clostridium perfringens</option>
            <option value="13">Clostridium chauvoei</option>
            <option value="14">Bacillus anthracis</option>
            <option value="15">Klebsiella oxytoca</option>
            <option value="16">Clostridium neonatale</option>
        </param>
        <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
        <param argument="--schema-id" type="integer" min="1" value="1" label="Schema ID"/>
    </inputs>
    <outputs>
        <data format="zip" name="schema" from_work_dir="schema_seed.zip" label="${tool.name} Schema files"/>
    </outputs>
    <tests>
        <test expect_exit_code="0">
            <param name="species_id" value="13"/>
            <param name="schema_id" value="1"/>
            <assert_stdout>
                <has_text text="Schema is now available at"/>
                <has_text text="Finished at"/>
            </assert_stdout>
            <output name="schema">
                <assert_contents>
                    <has_archive_member path="schema_seed/.*\.fasta" n="4446"/>
                    <has_archive_member path="schema_seed/short/.*\.fasta" n="2223"/>
                    <has_archive_member path="schema_seed/\.ns_config"/>
                    <has_archive_member path="schema_seed/\.schema_config"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        
chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.

The DownloadSchema module enables the download of schemas from the Chewie-NS server.


.. class:: infomark 

**Note**

The output schema files are in a zip file. This file can be used as input for other chewBBACA tools.

-----

Compressed versions of every schema in the Chewie-NS are also available for download:
 - through the `Chewie-NS public website`_
 - through the (/species/{species_id}/schemas/{schema_id}/zip) API endpoint in Swagger_
 - with a simple curl command (e.g.: curl -X GET "https://chewbbaca.online/NS/api/species/9/schemas/1/zip?request_type=download" -H  "accept: application/json")

.. _Chewie-NS public website: https://chewbbaca.online/
.. _Swagger: https://chewbbaca.online/api/NS/api/docs
    </help>
    <expand macro="citations" />
</tool>