annotate spatyper.xml @ 0:52d69f74b19e draft

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper commit a211c27b9f7386f8e43419ec22b88403498da26e

<tool id="spatyper" name="Generate spa type identification" version="@VERSION@+galaxy0" profile="21.01">
    <macros>
        <token name="@VERSION@">0.3.3</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">spatyper</requirement>
    </requirements>
    <command detect_errors="aggressive"> <![CDATA[
        spaTyper -f '${input1}' -r '${input2}' > '${output1}' 
    ]]> </command>
    <inputs>
        <param type="data" name="input1" format="fasta" label="SPA Fasta file" help="Staphylococcus aureus - staphylococcal protein A fasta file. This will be assigned a type based on its repeat region."/>
        <param type="data" name="input2" format="fasta" label="Repeats Library Multifasta" help="A multifasta representing a set of known repeat regions found in staphylococcal protein A. This can be downloaded at (http://spa.ridom.de/dynamic/sparepeats.fasta)"/>
    </inputs>
    <outputs>
        <data name="output1" format="txt" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="input.fasta"/>
            <param name="input2" value="sparepeats.fasta"/>
            <output name="output1">
                <assert_contents>
                    <has_text text = "t11215" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
::

    USAGE: spaTyper [-h] [-r REPEAT_FILE] [-o REPEAT_ORDER_FILE] [-d FOLDER] [-f FASTA [FASTA ...]] [-g GLOB] [-e] [--output OUTPUT] [--version] [--debug] [--info]

    spaTyper.py: Get spa types

    Version: 0.3.3
    License: GPLv3
    Prints spa type to stdout

    It will download sparepeats.fasta and spatypes.txt to repository directory 
    if files not provided or already in directory. It can be loaded as a python
    module. Python 3 version only.

    Options: -h     show this help message and exit
             -r     REPEAT_FILE (http://spa.ridom.de/dynamic/sparepeats.fasta)
             -o     REPEAT_ORDER_FILE (http://spa.ridom.de/dynamic/spatypes.txt)
             -d     Folder to save downloaded files from Ridom/Spa server
             -f     List of one or more fasta files.
             -g     Uses unix style pathname expansion to run spa typing on all files. If your shell autoexpands wildcards use -f.
             -e     Do PCR product enrichment. [Default: False]

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubseqtk,
  author = {HCGB},
  year = {2020},
  title = {spaTyper},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/HCGB-IGTP/spaTyper},
}</citation>
    </citations>
</tool>