annotate NSStats.xml @ 2:73c54f755a31 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 501c1cb91f4b91ec93e6df6e555323bbe8e2b703

<tool id="chewbbaca_nsstats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Retrieve basic information about the species and schemas in Chewie-NS</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        chewBBACA.py NSStats
            -m $mode
            #if $species_id != ""
            --sp $species_id 
            #end if
            #if $schema_id != ""
            --sc $schema_id
            #end if
            > 'NSStats.txt'
    ]]></command>
    <inputs>
        <param argument="--mode" type="select" label="Mode" optional="false">
            <option value="species">species</option>
            <option value="schemas">schemas</option>
        </param>
        <param argument="--species-id" type="select" label="Species ID" value="" optional="true">
            <expand macro="species_id"/>
        </param>
        <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
        <param argument="--schema-id" type="integer" min="1" value="" label="Schema ID" optional="true"/>
    </inputs>
    <outputs>
        <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name}"/>
    </outputs>
    <tests>
        <test expect_exit_code="0">
            <param name="mode" value="species" />
            <output name="NSStats">
                <assert_contents>
                    <has_text_matching expression="Streptococcus pyogenes\s+1\s+1\s+3044\s+398511"/>
                    <has_text_matching expression="Clostridium neonatale\s+16\s+1\s+2350\s+13115"/>
                </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 NSStats module enables the retrieval of information from the Chewie-NS server. Its main objective is to provide information about the list of species and schemas in Chewie-NS, so that users can quickly identify a schema of interest and download it.

    </help>
    <expand macro="citations" />
</tool>