annotate macros.xml @ 0:51916b7025ba draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"

<?xml version="1.0"?>
<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">r-gprofiler2</requirement>
            <requirement type="package" version="2.7.3">pandoc</requirement>
            <yield />
        </requirements>
    </xml>

    <token name="@TOOL_VERSION@">0.1.7</token>
    <token name="@VERSION@">@TOOL_VERSION@+galaxy10</token>

    <xml name="version_command">
        <version_command>
            Rscript -e 'library(gprofiler2); packageVersion("gprofiler2")' | sed 's/\[1\] //' | sed 's/.//;s/.$//'
        </version_command>
    </xml>

    <token name="@REFERENCES@"><![CDATA[

This tool is part of the `g:Profiler`_ from the `University of Tartu`_.

  .. _g:Profiler: https://biit.cs.ut.ee/gprofiler/
  .. _University of Tartu: https://ut.ee/en/

**Resources**
  * `A complete list of suppоrted organism IDs`_
  * `A complete list of supported namespaces`_

  .. _A complete list of suppоrted organism IDs: https://biit.cs.ut.ee/gprofiler/page/organism-list
  .. _A complete list of supported namespaces: https://biit.cs.ut.ee/gprofiler/page/namespaces-list

**gprofiler2 R tool**
  * https://CRAN.R-project.org/package=gprofiler2 — as CRAN package.
  * https://anaconda.org/conda-forge/r-gprofiler2 — as conda-forge package.

**Contact**
  * Contact us at [e-mail] for further help.

.. class:: warningmark

By default the tool makes requests to APIs of the latest g:Profiler instance with the most recent data release.
Please, use ’Tool Settings → Base URL’ to modify it in case you want to make use of older data versions. Also, if the
results should be pinned for reproducibility, we suggest to modify the base url to the last archived data version.

    ]]></token>

    <xml name="input">
        <param name="input" type="data" format="txt" label="Input is whitespace-separated list of genes, proteins, probes, term IDs or chromosomal regions." />
    </xml>
    <xml name="organism" token_name="organism" token_label="Organism"
         token_hsapiens_selected="true" token_mmusculus_selected="false">
        <conditional name="@NAME@">
            <param name="select_input_type" type="select" label="@LABEL@">
                <option value="select">Common organisms</option>
                <option value="input">Enter organism ID</option>
            </param>
            <when value="select">
                <param name="organism" type="select" label="Common organisms">
                    <option value="athaliana">Arabidopsis thaliana</option>
                    <option value="afumigatusa1163">Aspergillus fumigatus A1163</option>
                    <option value="btaurus">Bos taurus (Cow)</option>
                    <option value="celegans">Caenorhabditis elegans</option>
                    <option value="cfamiliaris">Canis lupus familiaris (Dog)</option>
                    <option value="drerio">Danio rerio (Zebrafish)</option>
                    <option value="dmelanogaster">Drosophila melanogaster</option>
                    <option value="ggallus">Gallus gallus (Chicken)</option>
                    <option value="hsapiens" selected="@HSAPIENS_SELECTED@">Homo sapiens (Human)</option>
                    <option value="mmusculus" selected="@MMUSCULUS_SELECTED@">Mus musculus (Mouse)</option>
                    <option value="osativa">Oryza sativa Japonica Group</option>
                    <option value="pteres">Pyrenophora teres f. teres 0-1 (Pyrenophora teres)</option>
                    <option value="rnorvegicus">Rattus norvegicus (Rat)</option>
                    <option value="scerevisiae">Saccharomyces cerevisiae</option>
                    <option value="zmays">Zea mays</option>
                </param>
            </when>
            <when value="input">
                <param name="organism" type="text" value="hsapiens" label="Enter organism ID" help="Organism IDs are constructed by concatenating the first letter of the generic name and the specific name. E.g., human — Homo sapiens — ’hsapiens’, mouse — Mus musculus — ’mmusculus’, thale cress — Arabidopsis thaliana — ’athaliana’. Check the help section below for the complete list of supported organism IDs." />
            </when>
        </conditional>
    </xml>

    <xml name="filter_na">
        <param name="filter_na" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Filter N/A" help="Whether to filter out results without a corresponding target name." />
    </xml>

    <xml name="tool_settings">
        <section name="tool_settings" title="Tool settings" expanded="false">
            <param type="text" name="base_url" label="Base URL" optional="true" help="Useful for overriding the default URL (http://biit.cs.ut.ee/gprofiler) with the beta (https://biit.cs.ut.ee/gprofiler_beta) or a compatible archived version (available starting from the version e94_eg41_p11, e.g. https://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11)." value="http://biit.cs.ut.ee/gprofiler" />
            <yield />
        </section>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">doi:10.1093/nar/gkz369</citation>
            <yield />
        </citations>
    </xml>
</macros>