diff data_manager/busco_options.xml @ 6:b2d2cba0dca6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit d46d2ec37b9b8f08d58472978c51b4c46e7ed18c

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/busco_options.xml	Fri Apr 04 10:12:28 2025 +0000
@@ -0,0 +1,47 @@
+<tool id="busco_fetcher_options" name="Busco options" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
+    <description></description>
+        <macros>
+        <token name="@TOOL_VERSION@">5.8.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $test:
+            busco --download_path test/ --download virus > /dev/null &&
+            #set db_path="./test"
+        #else
+            #set db_path=$cached_db.fields.path
+        #end if
+        python '$__tool_directory__/extract.py' '$db_path' '$cached_db' '$out_file'
+    ]]></command>
+    <inputs>
+        <param name="test" type="hidden"/>
+        <param name="cached_db" label="Cached database with lineage" type="select">
+            <options from_data_table="busco_database">
+                <validator message="No BUSCO database is available" type="no_options"/>
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" label="BUSCO options data manager: JSON"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="test" value="true"/>
+            <param name="cached_db" value="test"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="busco_database_options"/>
+                    <has_text text="Chordopoxvirinae"/>
+                    <has_text text="chordopoxvirinae_"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>This tool determines the possible choices of BUSCO lineages in a given BUSCO DB.</help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btv351</citation>
+    </citations>
+</tool>