annotate end_to_end.xml @ 0:ace74c46b80f draft

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/checkv/ commit 625d1e8699c69e5ee3caef0cc5c883a9d9e6ac91

<tool id="checkv_end_to_end" name="CheckV end to end" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description></description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.3</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">checkv</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">checkv</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        checkv end_to_end
            '$input'
            output
            -d '$reference.fields.path'
            --remove_tmp
            -t "\${GALAXY_SLOTS:-1}"
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz,fasta.bz2" label="Input nucleotide sequences in FASTA format"/>
        <param name="reference" type="select" label="CheckV reference data">
            <options from_data_table="checkv">
                <validator type="no_options" message="No reference data available. Contact your Galaxy admin"/>
            </options>
        </param>
        <param name="optional_outputs" type="select" optional="true" multiple="true" label="Optional outputs">
            <option value="completeness">Overview of how completeness was estimated</option>
            <option value="contamination"></option>
        </param>
    </inputs>
    <outputs>
        <data name="quality_summary" format="tabular" from_work_dir="output/quality_summary.tsv" label="${tool.name} on ${on_string}: Quality summary"/>
        <data name="completeness" format="tabular" from_work_dir="output/completeness.tsv" label="${tool.name} on ${on_string}: Completeness">
            <filter>optional_outputs and "completeness" in optional_outputs</filter>
        </data>
        <data name="contamination" format="tabular" from_work_dir="output/contamination.tsv" label="${tool.name} on ${on_string}: Contamination">
            <filter>optional_outputs and "contamination" in optional_outputs</filter>
        </data>
        <data name="complete_genomes" format="tabular" from_work_dir="output/complete_genomes.tsv" label="${tool.name} on ${on_string}: Complete Genomes"/>
        <data name="proviruses" format="fasta" from_work_dir="output/proviruses.fna" label="${tool.name} on ${on_string}: Proviruses"/>
        <data name="viruses" format="fasta" from_work_dir="output/viruses.fna" label="${tool.name} on ${on_string}: Viruses"/>
    </outputs>
    <tests>
        <!-- <test expect_num_outputs="4">
            <param name="input" value="test_sequences.fna"/>
            <param name="reference" value="1.5"/>
            <output name="quality_summary">
                <assert_contents>
                    <has_n_columns n="14"/>
                    <has_n_lines n="41"/>
                </assert_contents>
            </output>
            <output name="complete_genomes">
                <assert_contents>
                    <has_n_columns n="11"/>
                    <has_n_lines n="6"/>
                </assert_contents>
            </output>
            <output name="viruses">
                <assert_contents>
                    <has_line_matching expression="^>.*" n="39"/>
                </assert_contents>
            </output>
            <output name="proviruses">
                <assert_contents>
                    <has_line_matching expression="^>.*" n="1"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <param name="input" value="test_sequences.fna"/>
            <param name="reference" value="1.5"/>
            <param name="optional_outputs" value="completeness,contamination"/>
            <output name="quality_summary">
                <assert_contents>
                    <has_n_columns n="14"/>
                    <has_n_lines n="41"/>
                </assert_contents>
            </output>
            <output name="completeness">
                <assert_contents>
                    <has_n_columns n="15"/>
                    <has_n_lines n="41"/>
                </assert_contents>
            </output>
            <output name="contamination">
                <assert_contents>
                    <has_n_columns n="14"/>
                    <has_n_lines n="41"/>
                </assert_contents>
            </output>
            <output name="complete_genomes">
                <assert_contents>
                    <has_n_columns n="11"/>
                    <has_n_lines n="6"/>
                </assert_contents>
            </output>
            <output name="viruses">
                <assert_contents>
                    <has_line_matching expression="^>.*" n="39"/>
                </assert_contents>
            </output>
            <output name="proviruses">
                <assert_contents>
                    <has_line_matching expression="^>.*" n="1"/>
                </assert_contents>
            </output>
        </test> -->
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

CheckV is a fully automated command-line pipeline for assessing the quality of single-contig viral genomes, including identification of host contamination for integrated proviruses, estimating completeness for genome fragments, and identification of closed genomes.

There are 4 steps:

1. Remove host contamination on proviruses
   - Genes are first annotated as viral or microbial based on comparison to a custom database of HMMs
   -  CheckV scans over the contig (5' to 3') comparing gene annotations and GC content between a pair of adjacent gene windows
   -  This information is used to compute a score at each intergenic position and identify host-virus breakpoints
   -  Works best for contigs that are mostly viral

2. Estimate genome completeness

   - Proteins are first compared to the CheckV genome database using AAI (average amino acid identity)
   - After identifying the top hits, completeness is computed as a ratio between the contig length (or viral region length for proviruses) and the length of matched reference
   - A confidence level is reported based on the strength of the alignment
   - Generally, high- and medium-confidence estimates are quite accurate
   - Less frequently, your viral genome may not have a close match to the CheckV database; in these cases CheckV estimates the completeness based on the viral HMMs identified on the contig
   - Based on the HMMs found, CheckV returns the estimated range for genome completeness (e.g. 35% to 60% completeness), which represents the 90% confidence interval based on the distribution of lengths of reference genomes with the same viral HMMs

3.: Predict closed genomes

    - Direct terminal repeats (DTRs)
        - Repeated sequence of >20-bp at start/end of contig
        - Most trusted signature in our experience
        - May indicate circular genome or linear genome replicated from a circular template (i.e. concatamer)
    - Proviruses
        - Viral region with predicted host boundaries at 5' and 3' ends (see panel A)
        - Note: CheckV will not detect proviruses if host regions have already been removed (e.g. using VIBRANT or VirSorter)
    - Inverted terminal repeats (ITRs)
        - Repeated sequence of >20-bp at start/end of contig (3' repeat is inverted)
        - Least trusted signature
    - For all the methods above, CheckV also checks whether the contig is approximately the correct sequence length based on estimated completeness; this is important because terminal repeats can represent artifacts of metagenomic assembly

4. Summarize quality.

   - Based on the results of 1-3, CheckV generates a report file and assigns query contigs to one of five quality tiers (consistent with and expand upon the MIUViG quality tiers):

     - Complete
     - High-quality (>90% completeness)
     - Medium-quality (50-90% completeness)
     - Low-quality (<50% completeness)
     - Undetermined quality


Usage
.....


**Input**

- Viral contigs in fasta (or gz, bz2 compressed fasta).
- CheckV reference data

**Output**

- Quality Summary: Tabular file showing integrated results from the three main modules and should be the main output referred to.
- Complete genomes: Tabular overview of putative complete genomes identified.
- Viruses: Virus sequences
- Proviruses: Provirus sequences

Optional outputs:

- Completeness: detailed overview of how completeness was estimated
- Contamination:  detailed overview of how contamination was estimated
    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41587-020-00774-7</citation>
    </citations>
</tool>