diff data_manager/funannotate_options.xml @ 5:5459ec34767a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_funannotate commit 8341270dd36185ebf59d15282bc79f1215e936a4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/funannotate_options.xml	Fri Mar 07 22:33:29 2025 +0000
@@ -0,0 +1,61 @@
+<tool id="data_manager_funannotate_options" name="Funannotate options data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
+    <macros>
+        <token name="@TOOL_VERSION@">1.8.15</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement>
+    </requirements>
+    <version_command>funannotate check --show-versions</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $test:
+            funannotate setup -d ./test/ -i busco busco_outgroups -b eukaryota > /dev/null &&
+            #set db_path="./test"
+        #else
+            #set db_path=$database.fields.path
+        #end if
+        python '$__tool_directory__/extract.py' '$db_path' '$database' '$output_file'
+    ]]></command>
+    <inputs>
+        <param name="test" type="hidden" value="" help="Used for testing"/>
+        <param name="database" label="Funannotate database" type="select">
+            <options from_data_table="funannotate">
+                <column name="value" index="0" />
+                <column name="name" index="1" />
+                <column name="path" index="3" />
+                <filter type="sort_by" column="0" reverse_sort_order="true"/>
+                <!-- <filter type="static_value" column="2" value="1.0" /> -->
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="data_manager_json"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="test" value="true"/>
+            <param name="database" value="test"/>
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="busco_db" n="1"/>
+                    <has_text text="outgroup" n="6"/>
+                    <has_text text="trained_species" n="166"/>
+                </assert_contents>
+            </output>
+            <assert_stdout>
+                <has_line line="1 x busco_db"/>
+                <has_line line="166 x trained_species"/>
+                <has_line line="6 x outgroup"/>
+            </assert_stdout>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This data managers determines the options available in the select parameters of the funannotate tool
+        for a given funannotate DB in the funannotate data table
+
+        .. _funannotate: https://funannotate.readthedocs.io
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.4054262</citation>
+    </citations>
+</tool>