--- a/busco.xml	Mon Jul 26 21:29:40 2021 +0000
+++ b/busco.xml	Tue Nov 02 09:40:29 2021 +0000
@@ -1,5 +1,8 @@
 <tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>assess genome assembly and annotation completeness</description>
+    <xrefs>
+        <xref type="bio.tools">busco</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -22,7 +25,6 @@
 
 busco
 --in '${input}'
---lineage_dataset '${lineage_dataset}'
 --update-data
 --mode '${busco_mode.mode}'
 --out busco_galaxy
@@ -30,8 +32,10 @@
 --evalue ${adv.evalue}
 --limit ${adv.limit}
 
-#if $adv.auto_lineage:
-    $adv.auto_lineage
+#if $lineage.lineage_mode == "auto_detect":
+    $lineage.auto_lineage
+#else if $lineage.lineage_mode == "select_lineage":
+    --lineage_dataset '${lineage.lineage_dataset}'
 #end if
 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
 
@@ -96,18 +100,28 @@
             <when value="prot" />
         </conditional>
 
-        <param argument="--lineage_dataset" type="select" label="Lineage">
-            <expand macro="lineages" />
-        </param>
+        <conditional name="lineage">
+            <param name="lineage_mode" type="select" label="Auto-detect or select lineage?" help="Let BUSCO decide the best lineage automatically, or select from known lineage">
+                <option value="auto_detect">Auto-detect</option>
+                <option value="select_lineage">Select lineage</option>
+            </param>
+            <when value="auto_detect">
+                <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">
+                    <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
+                    <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
+                    <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
+                </param>
+            </when>
+            <when value="select_lineage">
+                <param argument="--lineage_dataset" type="select" label="Lineage">
+                    <expand macro="lineages" />
+                </param>
+            </when>
+        </conditional>
 
         <section name="adv" title="Advanced Options" expanded="False">
             <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
             <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
-            <param name="auto_lineage" type="select" optional="true" label="Run auto-lineage to find optimal lineage path">
-                <option value="--auto-lineage">Run auto-lineage to find optimum lineage path</option>
-                <option value="--auto-lineage-prok">Run auto-lineage just on non-eukaryote trees to find optimum lineage path</option>
-                <option value="--auto-lineage-euk">Run auto-placement just on eukaryote tree to find optimum lineage path</option>
-            </param>
             <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
                 <option value="short_summary">short summary text</option>
                 <option value="missing">list with missing IDs</option>
@@ -130,7 +144,10 @@
     <tests>
         <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />
-            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="lineage">
+                <param name="lineage_mode" value="select_lineage" />
+                <param name="lineage_dataset" value="arthropoda_odb10" />
+            </conditional>
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
@@ -150,7 +167,10 @@
         </test>
         <test expect_num_outputs="4">
             <param name="input" value="proteome.fa" />
-            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="lineage">
+                <param name="lineage_mode" value="select_lineage" />
+                <param name="lineage_dataset" value="arthropoda_odb10" />
+            </conditional>
             <conditional name="busco_mode">
                 <param name="mode" value="prot" />
             </conditional>
@@ -164,22 +184,27 @@
         </test>
         <test expect_num_outputs="4">
             <param name="input" value="transcriptome.fa" />
-            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="lineage">
+                <param name="lineage_mode" value="select_lineage" />
+                <param name="lineage_dataset" value="arthropoda_odb10" />
+            </conditional>
             <conditional name="busco_mode">
                 <param name="mode" value="tran" />
             </conditional>
             <section name="adv">
-                <param name="auto_lineage" value="--auto-lineage" />
                 <param name="outputs" value="short_summary,missing,image" />
             </section>
-            <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4" />
-            <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4" />
-            <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4" />
+            <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
+            <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
+            <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
             <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
         </test>
         <test expect_num_outputs="2">
             <param name="input" value="genome.fa" />
-            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="lineage">
+                <param name="lineage_mode" value="select_lineage" />
+                <param name="lineage_dataset" value="arthropoda_odb10" />
+            </conditional>
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
@@ -198,7 +223,10 @@
         </test>
         <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />
-            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="lineage">
+                <param name="lineage_mode" value="select_lineage" />
+                <param name="lineage_dataset" value="arthropoda_odb10" />
+            </conditional>
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
@@ -218,7 +246,10 @@
         </test>
         <test expect_num_outputs="4">
             <param name="input" value="genome.fa" />
-            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="lineage">
+                <param name="lineage_mode" value="select_lineage" />
+                <param name="lineage_dataset" value="arthropoda_odb10" />
+            </conditional>
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
                 <conditional name="use_augustus">
@@ -228,11 +259,31 @@
             <section name="adv">
                 <param name="outputs" value="short_summary,missing,image" />
             </section>
-            <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="4" />
-            <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="4" />
-            <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="4" />
+            <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />
+            <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
+            <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
             <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
         </test>
+        <test expect_num_outputs="4">
+            <param name="input" value="genome.fa" />
+            <conditional name="lineage">
+                <param name="lineage_mode" value="auto_detect" />
+                <param name="auto_lineage" value="--auto-lineage" />
+            </conditional>
+            <conditional name="busco_mode">
+                <param name="mode" value="geno" />
+                <conditional name="use_augustus">
+                    <param name="use_augustus_selector" value="no" />
+                </conditional>
+            </conditional>
+            <section name="adv">
+                <param name="outputs" value="short_summary,missing,image" />
+            </section>
+            <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="4" />
+            <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="0" />
+            <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="0" />
+            <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
+        </test>
     </tests>
     <help><![CDATA[