view extract_kraken_reads.xml @ 0:5ca43a5fac32 draft

planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/KrakenTools

<tool id="extract_kraken_reads" name="extract_kraken_reads" version="0.1.0">
    <description>Extract reads classified at any user-specified taxonomy IDs.</description>
    <requirements>
        <requirement type="package" version="1.2">krakentools</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
extract_kraken_reads.py
-k '$classification'
-s '$seq'
-t $taxid
--max $maxreads
-o '$output1'
    ]]>
    </command>
    <inputs>
        <param type="data" name="classification" format="tabular" label="Kraken classification output" />
        <param type="data" name="seq" format="fasta,fastq" label="Select the same fasta/fastq reads used" />
        <param type="text" name="taxid" label="Taxonomy ID[s] of reads to extract (space-delimited)" />
        <param name="maxreads" type="integer" value="10" min="1" label="Maximum number of reads to save" />
    </inputs>
    <outputs>
        <data name="output1" format="fasta" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="classification" value="kraken2_class.tsv" />
            <param name="seq" value="tid1613.fasta" />
            <param name="taxid" value="1613" />
            <param name="taxid" value="1" />
            <output name="output1" file="out.fasta" />
        </test>
    </tests>
    <help>
<![CDATA[
.. class:: infomark

**What it does**

This program extract reads classified at any user-specified taxonomy IDs. User must specify the Kraken output file, the sequence file(s), and at least one taxonomy ID.

As of April 19, 2021, this script is compatible with KrakenUniq/Kraken2Uniq reports.
]]>
    </help>
    <citations>
        <citation type="bibtex">
@misc{githubKrakenTools,
  title = {KrakenTools},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/jenniferlu717/KrakenTools},
}</citation>
    </citations>
</tool>