annotate plasflow.xml @ 2:1d2a91ab28b7 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow commit 469db427c69fa33e2e0acf042d8a52f552551261

<tool id="PlasFlow" name="PlasFlow" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
    <description>Prediction of plasmid sequences in metagenomic contigs</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">plasflow</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">plasflow</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
## PlasFlow supports gz only partially 
## https://github.com/smaegol/PlasFlow/blob/45604ff637c65f709dabff63e665fa60896be241/PlasFlow.py#L444
#if $readFile.ext == "fasta.gz"
    gunzip -c '$readFile' > 'reads.fasta' &&
#else
    ln -s '$readFile' 'reads.fasta' &&
#end if

PlasFlow.py
--input 'reads.fasta'
--output 'output'
--threshold '$threshold'
    ]]></command>
    <inputs>
        <param name="readFile" type="data" format="fasta,fasta.gz" optional="true" label="Contig Sequences" />
        <param argument="threshold" type="float" value="0.7" min="0" max="1" label="Threshold for probability filtering"/>
    </inputs>
    <outputs>
        <data name="probability_table" from_work_dir="output" format="tabular" label="${tool.name} on ${on_string}: Probability table" />
        <data name="chromosomes" from_work_dir="output_chromosomes.fasta" format="fasta" label="${tool.name} on ${on_string}: Chromosomes" />
        <data name="plasmids" from_work_dir="output_plasmids.fasta" format="fasta" label="${tool.name} on ${on_string}: Plasmids" />
        <data name="unclassified" from_work_dir="output_unclassified.fasta" format="fasta" label="${tool.name} on ${on_string}: Unclassified" />
    </outputs>
    <tests>
        <test>
            <param name="readFile" value="test.fasta" ftype="fasta"/>
            <param name="threshold" value="0.7"/>
            <output name="probability_table" value="output" compare="re_match"/>
            <output name="chromosomes" value="output_chromosomes.fasta"/>
            <output name="plasmids" value="output_plasmids.fasta"/>
            <output name="unclassified" value="output_unclassified.fasta"/>
        </test>
        <test>
            <param name="readFile" value="test.fasta.gz" ftype="fasta.gz"/>
            <param name="threshold" value="0.7"/>
            <output name="probability_table" value="output" compare="re_match"/>
            <output name="chromosomes" value="output_chromosomes.fasta"/>
            <output name="plasmids" value="output_plasmids.fasta"/>
            <output name="unclassified" value="output_unclassified.fasta"/>
        </test>
    </tests>
    <help><![CDATA[
PlasFlow is a set of scripts used for prediction of plasmid sequences in
metagenomic contigs. It relies on the neural network models trained on full
genome and plasmid sequences and is able to differentiate between plasmids and
chromosomes with accuracy reaching 96%. It outperforms other available solutions
for plasmids recovery from metagenomes and incorporates the thresholding which
allows for exclusion of incertain predictions.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkx1321</citation>
    </citations>
</tool>