view plasclass.xml @ 0:8a97b4648968 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass commit 8cec6b221914a96102b6d09b51e95626d43a9f8c

<tool id="plasclass" name="PlasClass" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description>for plasmid/chromosome classification</description>
    <macros>
        <token name="@TOOL_VERSION@">0.1.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@PROFILE@">24.1</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">PlasClass</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">plasclass</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
classify_fasta.py
    --fasta '$fasta'
    --outfile '$outfile'
    --num_processes "\${GALAXY_SLOTS:-1}"
    ]]></command>
    <inputs>
        <param argument="--fasta" type="data" format="fasta" label="Sequences to be classified"/>
    </inputs>
    <outputs>
        <data name="outfile" format="tabular"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="fasta" value="test.fa"/>
            <output name="outfile" ftype="tabular">
                <assert_contents>
                    <has_text text="EDGE_1998488_length_236_cov_0.817680"/>
                    <has_n_lines n="62"/>
                    <has_n_columns n="2"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

PlasClass is a cutting-edge plasmid classifier designed to address the challenges of distinguishing between 
plasmid and bacterial genome sequences in metagenomic and isolate assemblies. Many bacteria contain plasmids, 
but identifying contigs that originate from plasmids can be particularly difficult in metagenomic assembly, 
where the origin of contigs is often unknown. 

**Input**

- FASTA file with sequences to classify

**Output**

- A tabular separated file with each line containing a sequence header and the corresponding score. The sequences are in the same order as in the input FASTA file.

    ]]></help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1007781</citation>
    </citations>
</tool>