annotate garnett_macros.xml @ 1:1023eae1b147 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 241c850301f8094f6aa0016e2335a8b550c29aed"

<macros>
    <token name="@TOOL_VERSION@">0.2.8</token>
    <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/garnett/docs/</token>
    <token name="@PROFILE@">18.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="0.0.5">garnett-cli</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="version">
        <version_command><![CDATA[
        echo $(R --version | grep version | grep -v GNU)", garnett version" $(R --vanilla --slave -e "library(garnett); cat(sessionInfo()\$otherPkgs\$garnett\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
        ]]></version_command>
    </xml>
    <token name="@VERSION_HISTORY@"><![CDATA[
    **Version history**
    0.2.8+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
    ]]></token>
    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @article{,
                url = {https://doi.org/10.1038/s41592-019-0535-3},
                author = {Hannah A. Pliner and Jay Shendure and Cole Trapnell},
                title = {Supervised classification enables rapid annotation of cell atlases},
                journal = {Nature Methods}
            }
        </citation>
            <citation type="bibtex">
                @misc{githubgarnett-cli.git,
                    author = {Andrey Solovyev, EBI Gene Expression Team},
                    year = {2019},
                    title = {garnett-cli: command line interface for Garnett tool},
                    publisher = {GitHub},
                    journal = {GitHub repository},
                    url = {https://github.com/ebi-gene-expression-group/garnett-cli.git},
                  }
            </citation>
            <yield />
            <citation type="doi">10.1101/2020.04.08.032698</citation>
        </citations>
    </xml>
</macros>