Mercurial > repos > iuc > data_manager_omamer

diff data_manager/omamer.xml @ 0:d28438704310 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
author: iuc
date: Wed, 14 Aug 2024 15:42:38 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/omamer.xml	Wed Aug 14 15:42:38 2024 +0000
@@ -0,0 +1,45 @@
+<tool id="data_manager_omamer" name="OMAmer data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <version_command></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/omamer.py'
+        --name '$name'
+        --json '$output_file'
+        --version '@TOOL_VERSION@'
+    ]]></command>
+    <inputs>
+        <param name="output_dir" type="text" label="Output Directory" value=""/>
+        <param name="name" type="select" label="Database">
+            <option value="Primates_v2.0.0">Primates_v2.0.0</option>
+            <option value="Viridiplantae_v2.0.0">Viridiplantae_v2.0.0</option>
+            <option value="Metazoa_v2.0.0">Metazoa_v2.0.0</option>
+            <option value="LUCA_v0.2.5">LUCA_v0.2.5</option>
+            <option value="LUCA_v2.0.0">LUCA_v2.0.0</option>
+            <option value="Saccharomyceta">Saccharomyceta</option>
+            <option value="Homininae">Homininae</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output_file" format="data_manager_json" label="OMAmer data manager: JSON"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="output_dir" value="test_galaxy"/>
+            <param name="name" value="Primates_v2.0.0"/>
+            <output name="output_file" file="out.json"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        This data manager retrieves data from various pre-built databases.
+
+        .. _omamer: https://github.com/DessimozLab/omamer
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btab219</citation>
+    </citations>
+</tool>