--- a/data_manager/busco_fetcher.xml	Sun Nov 22 12:47:50 2020 +0000
+++ b/data_manager/busco_fetcher.xml	Mon Apr 24 12:26:46 2023 +0000
@@ -1,62 +1,43 @@
-<?xml version="1.0"?>
-<tool id="busco_fetcher" name="Busco" tool_type="manage_data" version="1.0.0">
+<tool id="busco_fetcher" name="Busco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01">
     <description>dataset dowloader</description>
-    <command detect_errors="exit_code">
-    <![CDATA[
-        python '$__tool_directory__/data_manager.py' --out '${out_file}'
-            --url 'http://busco.ezlab.org/datasets/${dataset}.tar.gz'
-            --name '${dataset}'
-    ]]>
-    </command>
+        <macros>
+        <token name="@TOOL_VERSION@">5.4.6</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/data_manager.py'
+            --database '$lineage'
+            --name $lineage+\$(date +'%Y-%m-%d-%H%M%S')
+            --json '$out_file'
+            --version '@TOOL_VERSION@'
+    ]]></command>
     <inputs>
-        <param name="dataset" type="select" label="Choose dataset to download">
-            <option value="eukaryota_odb9">eukaryota</option>
-            <option value="metazoa_odb9">metazoa</option>
-            <option value="nematoda_odb9">nematoda</option>
-            <option value="arthropoda_odb9">arthropoda</option>
-            <option value="insecta_odb9">insecta</option>
-            <option value="endopterygota_odb9">endopterygota</option>
-            <option value="hymenoptera_odb9">hymenoptera</option>
-            <option value="diptera_odb9">diptera</option>
-            <option value="vertebrata_odb9">vertebrata</option>
-            <option value="actinopterygii_odb9">actinopterygii</option>
-            <option value="tetrapoda_odb9">tetrapoda</option>
-            <option value="aves_odb9">aves</option>
-            <option value="mammalia_odb9">mammalia</option>
-            <option value="euarchontoglires_odb9">euarchontoglires</option>
-            <option value="laurasiatheria_odb9">laurasiatheria</option>
-            <option value="embryophyta_odb9">embryophyta</option>
-            <option value="protists_ensembl">protists</option>
-            <option value="alveolata_stramenophiles_ensembl">alveolata</option>
-            <option value="fungi_odb9">fungi</option>
-            <option value="microsporidia_odb9">microsporidia</option>
-            <option value="dikarya_odb9">dikarya</option>
-            <option value="ascomycota_odb9">ascomycota</option>
-            <option value="pezizomycotina_odb9">pezizomycotina</option>
-            <option value="eurotiomycetes_odb9">eurotiomycetes</option>
-            <option value="sordariomyceta_odb9">sordariomyceta</option>
-            <option value="saccharomyceta_odb9">saccharomyceta</option>
-            <option value="saccharomycetales_odb9">saccharomycetales</option>
-            <option value="basidiomycota_odb9">basidiomycota</option>
-            <option value="bacteria_odb9">bacteria</option>
-            <option value="proteobacteria_odb9">proteobacteria</option>
-            <option value="rhizobiales_odb9">rhizobiales</option>
-            <option value="betaproteobacteria_odb9">betaproteobacteria</option>
-            <option value="gammaproteobacteria_odb9">gammaproteobacteria</option>
-            <option value="enterobacteriales_odb9">enterobacteriales</option>
-            <option value="deltaepsilonsub_odb9">deltaepsilonsub</option>
-            <option value="actinobacteria_odb9">actinobacteria</option>
-            <option value="cyanobacteria_odb9">cyanobacteria</option>
-            <option value="firmicutes_odb9">firmicutes</option>
-            <option value="clostridia_odb9">clostridia</option>
-            <option value="lactobacillales_odb9">lactobacillales</option>
-            <option value="bacillales_odb9">bacillales</option>
-            <option value="bacteroidetes_odb9">bacteroidetes</option>
-            <option value="spirochaetes_odb9">spirochaetes</option>
-            <option value="tenericutes_odb9">tenericutes</option>
+        <param name="lineage" 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>
     </inputs>
     <outputs>
-        <data name="out_file" format="data_manager_json" />
+        <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="5.4.6"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>This tool downloads the BUSCO databases.</help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btv351</citation>
+    </citations>
 </tool>