diff data_manager/busco_fetcher.xml @ 8:29548c43fb33 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_busco/ commit 32f1099f18b41bf1efd1a039daf732809c77269e

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/busco_fetcher.xml	Tue Apr 22 13:11:38 2025 +0000
@@ -0,0 +1,74 @@
+<tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="23.1">
+    <description>dataset dowloader</description>
+        <macros>
+        <token name="@TOOL_VERSION@">5.8.0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        busco --download_path '$out_file.extra_files_path' --download '$lineage' &&
+        ## remove unwanted lineage folders and placement files
+        ## https://gitlab.com/ezlab/busco/-/issues/784
+        if [ -d '$out_file.extra_files_path'/lineages ]; then
+            find '$out_file.extra_files_path'/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -exec rm -rf {} \;;
+        fi &&
+        if [ -d '$out_file.extra_files_path'/placement_files ]; then
+            find '$out_file.extra_files_path'/placement_files/ -mindepth 1 -maxdepth 1 ! -name '*_$datasets_version*' -delete;
+        fi &&
+        ## unpack faa.gz files ready to use
+        ## https://gitlab.com/ezlab/busco/-/issues/789
+        if [ -d '$out_file.extra_files_path'/lineages ]; then
+            find '$out_file.extra_files_path'/lineages/ -name "*.faa.gz" -exec gunzip {} \;;
+        fi
+        && cp '$dmjson' '$out_file' 
+    ]]></command>
+    <configfiles>
+        <configfile name="dmjson"><![CDATA[
+#from datetime import datetime
+    {
+      "data_tables":{
+        "busco_database":[
+          {
+            "value":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
+            "name":"$lineage $datasets_version #echo datetime.now().strftime('%Y-%m-%d-%H%M%S')#",
+            "version":"@TOOL_VERSION@",
+            "path":"$out_file.extra_files_path"
+          }
+        ]
+      }
+    }]]>
+            </configfile>
+        </configfiles>
+    <inputs>
+        <param name="lineage" argument="--download" type="select" label="Select the lineage to be downloaded">
+            <option value="all">All</option>
+            <option value="prokaryota">Prokaryota</option>
+            <option value="eukaryota">Eukaryota</option>
+            <option value="virus">Virus</option>
+        </param>
+        <param argument="--datasets_version" type="select" label="OrthoDB version" help="By March 2025 OrthoDB 12 datasets were only available for Prokaryota (https://busco-data2.ezlab.org/v5/data/)">
+            <option value="odb10" selected="true">OrthoDB 10</option>
+            <option value="odb12">OrthoDB 12</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" label="BUSCO data manager: JSON"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="lineage" value="virus"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="virus"/>
+                    <has_text text="5.8.0"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>This tool downloads the BUSCO databases.</help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btv351</citation>
+    </citations>
+</tool>