diff macros.xml @ 0:f83a08dff6f0 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Nov 14 06:01:29 2019 -0500
@@ -0,0 +1,101 @@
+<?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>