# HG changeset patch
# User iuc
# Date 1673530138 0
# Node ID bb935709506a3e154cbf7ad4c84adf526b1268b8
# Parent  41030a6c03b7f0c7d0d249a6867a9e50fb8ae97b
planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe

diff -r 41030a6c03b7 -r bb935709506a busco.xml
--- a/busco.xml	Mon Apr 11 09:02:11 2022 +0000
+++ b/busco.xml	Thu Jan 12 13:28:58 2023 +0000
@@ -1,11 +1,11 @@
 <tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>assess genome assembly and annotation completeness</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
     <xrefs>
         <xref type="bio.tools">busco</xref>
     </xrefs>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
         <requirement type="package" version="1.34">tar</requirement>
@@ -13,16 +13,21 @@
     </requirements>
     <version_command>busco --version</version_command>
     <command><![CDATA[
+
+#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
+
 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
 
-#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes' and $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
+#if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
     ## Using an augustus model from history, we need to unzip it and let augustus find it
     mkdir -p 'augustus_dir/species/' &&
     tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
 #end if
 
+#end if
+
 busco
 --in '${input}'
 --update-data
@@ -59,6 +64,14 @@
     generate_plot.py -wd BUSCO_summaries -rt specific
 #end if
 
+#if $outputs and 'gff' in $outputs:
+    &&
+    echo "\##gff-version 3" > busco_output.gff
+    &&
+    ## gff files can be absent
+    cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
+#end if
+
 ]]>    </command>
     <inputs>
         <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." />
@@ -123,6 +136,7 @@
             <option value="short_summary" selected="true">short summary text</option>
             <option value="missing">list with missing IDs</option>
             <option value="image">summary image</option>
+            <option value="gff">gff</option>
         </param>
 
         <section name="adv" title="Advanced Options" expanded="False">
@@ -141,9 +155,12 @@
         <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
             <filter>outputs and 'image' in outputs</filter>
         </data>
+        <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
+            <filter>outputs and 'gff' in outputs</filter>
+        </data>
     </outputs>
     <tests>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="4">
             <param name="input" value="genome.fa" />
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
@@ -155,16 +172,22 @@
                     <param name="use_augustus_selector" value="yes" />
                 </conditional>
             </conditional>
-            <param name="outputs" value="short_summary,missing" />
+            <param name="outputs" value="short_summary,missing,gff" />
             <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
             <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_gff">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_text text="##gff-version 3" />
+                </assert_contents>
+            </output>
             <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
                 <assert_contents>
                     <has_text text="# BUSCO version is: @TOOL_VERSION@" />
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="5">
             <param name="input" value="proteome.fa" />
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
@@ -173,13 +196,19 @@
             <conditional name="busco_mode">
                 <param name="mode" value="prot" />
             </conditional>
-            <param name="outputs" value="short_summary,missing,image" />
+            <param name="outputs" value="short_summary,missing,image,gff" />
             <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" />
             <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
             <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
+            <output name="busco_gff">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_text text="##gff-version 3" />
+                </assert_contents>
+            </output>
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="5">
             <param name="input" value="transcriptome.fa" />
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
@@ -188,13 +217,14 @@
             <conditional name="busco_mode">
                 <param name="mode" value="tran" />
             </conditional>
-            <param name="outputs" value="short_summary,missing,image" />
+            <param name="outputs" value="short_summary,missing,image,gff" />
             <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" />
+            <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
         </test>
-        <test expect_num_outputs="2">
+        <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
@@ -210,9 +240,15 @@
                     </conditional>
                 </conditional>
             </conditional>
-            <param name="outputs" value="short_summary" />
+            <param name="outputs" value="short_summary,gff" />
             <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
             <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_gff">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                    <has_text text="##gff-version 3" />
+                </assert_contents>
+            </output>
         </test>
         <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />
@@ -235,7 +271,7 @@
             <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="5">
             <param name="input" value="genome.fa" />
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
@@ -247,13 +283,14 @@
                     <param name="use_augustus_selector" value="no" />
                 </conditional>
             </conditional>
-            <param name="outputs" value="short_summary,missing,image" />
+            <param name="outputs" value="short_summary,missing,image,gff" />
             <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" />
+            <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" />
         </test>
-        <test expect_num_outputs="4">
+        <test expect_num_outputs="5">
             <param name="input" value="genome.fa" />
             <conditional name="lineage">
                 <param name="lineage_mode" value="auto_detect" />
@@ -265,11 +302,12 @@
                     <param name="use_augustus_selector" value="no" />
                 </conditional>
             </conditional>
-            <param name="outputs" value="short_summary,missing,image" />
+            <param name="outputs" value="short_summary,missing,image,gff" />
             <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />
             <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" />
             <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />
             <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
+            <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />
         </test>
     </tests>
     <help><![CDATA[
diff -r 41030a6c03b7 -r bb935709506a macros.xml
--- a/macros.xml	Mon Apr 11 09:02:11 2022 +0000
+++ b/macros.xml	Thu Jan 12 13:28:58 2023 +0000
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">5.3.2</token>
+    <token name="@TOOL_VERSION@">5.4.4</token>
     <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="citations">
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results/full_table
--- a/test-data/genome_results/full_table	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/genome_results/full_table	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results/missing_buscos_list
--- a/test-data/genome_results/missing_buscos_list	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/genome_results/missing_buscos_list	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results/short_summary
--- a/test-data/genome_results/short_summary	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/genome_results/short_summary	Thu Jan 12 13:28:58 2023 +0000
@@ -1,7 +1,7 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmpctznxi43/files/9/e/c/dataset_9ec37448-e146-4536-b66f-9082e1734ea4.dat
-# BUSCO was run in mode: genome
+# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_22.dat
+# BUSCO was run in mode: euk_genome_aug
 # Gene predictor used: augustus
 
 	***** Results: *****
@@ -14,11 +14,22 @@
 	1012	Missing BUSCOs (M)			   
 	1013	Total BUSCO groups searched		   
 
+Assembly Statistics:
+	1	Number of scaffolds
+	1	Number of contigs
+	62370	Total length
+	0.000%	Percent gaps
+	62 KB	Scaffold N50
+	62 KB	Contigs N50
+
+
 Dependencies and versions:
 	hmmsearch: 3.1
-	makeblastdb: 2.12.0+
-	tblastn: 2.12.0+
-	augustus: 3.4.0
+	bbtools: 39.01
+	makeblastdb: 2.13.0+
+	tblastn: 2.13.0+
+	augustus: 3.5.0
 	gff2gbSmallDNA.pl: None
 	new_species.pl: None
 	etraining: None
+	busco: 5.4.4
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk/full_table
--- a/test-data/genome_results_metaeuk/full_table	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/genome_results_metaeuk/full_table	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk/missing_buscos_list
--- a/test-data/genome_results_metaeuk/missing_buscos_list	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/genome_results_metaeuk/missing_buscos_list	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk/out.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_metaeuk/out.gff	Thu Jan 12 13:28:58 2023 +0000
@@ -0,0 +1,13 @@
+##gff-version 3
+sample	MetaEuk	gene	40256	42071	198	+	.	Target_ID=68987at6656;TCS_ID=68987at6656|sample|+|40255
+sample	MetaEuk	mRNA	40256	42071	198	+	.	Target_ID=68987at6656;TCS_ID=68987at6656|sample|+|40255_mRNA;Parent=68987at6656|sample|+|40255
+sample	MetaEuk	exon	40256	40390	49	+	.	Target_ID=68987at6656;TCS_ID=68987at6656|sample|+|40255_exon_0;Parent=68987at6656|sample|+|40255_mRNA
+sample	MetaEuk	CDS	40256	40390	49	+	.	Target_ID=68987at6656;TCS_ID=68987at6656|sample|+|40255_CDS_0;Parent=68987at6656|sample|+|40255_exon_0
+sample	MetaEuk	exon	40653	41168	94	+	.	Target_ID=68987at6656;TCS_ID=68987at6656|sample|+|40255_exon_1;Parent=68987at6656|sample|+|40255_mRNA
+sample	MetaEuk	CDS	40653	41168	94	+	.	Target_ID=68987at6656;TCS_ID=68987at6656|sample|+|40255_CDS_1;Parent=68987at6656|sample|+|40255_exon_1
+sample	MetaEuk	exon	41718	42071	65	+	.	Target_ID=68987at6656;TCS_ID=68987at6656|sample|+|40255_exon_2;Parent=68987at6656|sample|+|40255_mRNA
+sample	MetaEuk	CDS	41718	42071	65	+	.	Target_ID=68987at6656;TCS_ID=68987at6656|sample|+|40255_CDS_2;Parent=68987at6656|sample|+|40255_exon_2
+sample	MetaEuk	gene	34846	35679	545	-	.	Target_ID=94238at6656_7227_0:001f92;TCS_ID=94238at6656_7227_0:001f92|sample|-|34845
+sample	MetaEuk	mRNA	34846	35679	545	-	.	Target_ID=94238at6656_7227_0:001f92;TCS_ID=94238at6656_7227_0:001f92|sample|-|34845_mRNA;Parent=94238at6656_7227_0:001f92|sample|-|34845
+sample	MetaEuk	exon	34846	35679	545	-	.	Target_ID=94238at6656_7227_0:001f92;TCS_ID=94238at6656_7227_0:001f92|sample|-|34845_exon_0;Parent=94238at6656_7227_0:001f92|sample|-|34845_mRNA
+sample	MetaEuk	CDS	34846	35679	545	-	.	Target_ID=94238at6656_7227_0:001f92;TCS_ID=94238at6656_7227_0:001f92|sample|-|34845_CDS_0;Parent=94238at6656_7227_0:001f92|sample|-|34845_exon_0
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk/short_summary
--- a/test-data/genome_results_metaeuk/short_summary	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/genome_results_metaeuk/short_summary	Thu Jan 12 13:28:58 2023 +0000
@@ -1,7 +1,7 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmpctznxi43/files/9/6/4/dataset_96441510-fb85-41dd-a4ce-8a20d74173a9.dat
-# BUSCO was run in mode: genome
+# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_28.dat
+# BUSCO was run in mode: euk_genome_met
 # Gene predictor used: metaeuk
 
 	***** Results: *****
@@ -14,6 +14,17 @@
 	1011	Missing BUSCOs (M)			   
 	1013	Total BUSCO groups searched		   
 
+Assembly Statistics:
+	1	Number of scaffolds
+	1	Number of contigs
+	62370	Total length
+	0.000%	Percent gaps
+	62 KB	Scaffold N50
+	62 KB	Contigs N50
+
+
 Dependencies and versions:
 	hmmsearch: 3.1
-	metaeuk: 4.a0f584d
+	bbtools: 39.01
+	metaeuk: 6.a5d39d9
+	busco: 5.4.4
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk/summary.png
Binary file test-data/genome_results_metaeuk/summary.png has changed
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk_auto/full_table
--- a/test-data/genome_results_metaeuk_auto/full_table	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/genome_results_metaeuk_auto/full_table	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.3.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255)
 # Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length
 39650at2759	Missing
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk_auto/missing_buscos_list
--- a/test-data/genome_results_metaeuk_auto/missing_buscos_list	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/genome_results_metaeuk_auto/missing_buscos_list	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.3.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255)
 # Busco id
 1001705at2759
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk_auto/out.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_metaeuk_auto/out.gff	Thu Jan 12 13:28:58 2023 +0000
@@ -0,0 +1,5 @@
+##gff-version 3
+sample	MetaEuk	gene	34846	35679	545	-	.	Target_ID=1053181at2759_7227_0:001f92;TCS_ID=1053181at2759_7227_0:001f92|sample|-|34845
+sample	MetaEuk	mRNA	34846	35679	545	-	.	Target_ID=1053181at2759_7227_0:001f92;TCS_ID=1053181at2759_7227_0:001f92|sample|-|34845_mRNA;Parent=1053181at2759_7227_0:001f92|sample|-|34845
+sample	MetaEuk	exon	34846	35679	545	-	.	Target_ID=1053181at2759_7227_0:001f92;TCS_ID=1053181at2759_7227_0:001f92|sample|-|34845_exon_0;Parent=1053181at2759_7227_0:001f92|sample|-|34845_mRNA
+sample	MetaEuk	CDS	34846	35679	545	-	.	Target_ID=1053181at2759_7227_0:001f92;TCS_ID=1053181at2759_7227_0:001f92|sample|-|34845_CDS_0;Parent=1053181at2759_7227_0:001f92|sample|-|34845_exon_0
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk_auto/short_summary
--- a/test-data/genome_results_metaeuk_auto/short_summary	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/genome_results_metaeuk_auto/short_summary	Thu Jan 12 13:28:58 2023 +0000
@@ -1,7 +1,7 @@
-# BUSCO version is: 5.3.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmp5e3tdhzs/files/c/9/b/dataset_c9b61090-5a2d-4dd0-8fd1-d147a4e1573c.dat
-# BUSCO was run in mode: genome
+# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_34.dat
+# BUSCO was run in mode: euk_genome_met
 # Gene predictor used: metaeuk
 
 	***** Results: *****
@@ -14,7 +14,18 @@
 	254	Missing BUSCOs (M)			   
 	255	Total BUSCO groups searched		   
 
+Assembly Statistics:
+	1	Number of scaffolds
+	1	Number of contigs
+	62370	Total length
+	0.000%	Percent gaps
+	62 KB	Scaffold N50
+	62 KB	Contigs N50
+
+
 Dependencies and versions:
 	hmmsearch: 3.1
+	bbtools: 39.01
 	prodigal: 2.6.3
-	metaeuk: 5.34c21f2
+	busco: 5.4.4
+	metaeuk: 6.a5d39d9
diff -r 41030a6c03b7 -r bb935709506a test-data/genome_results_metaeuk_auto/summary.png
Binary file test-data/genome_results_metaeuk_auto/summary.png has changed
diff -r 41030a6c03b7 -r bb935709506a test-data/proteome_results/full_table
--- a/test-data/proteome_results/full_table	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/proteome_results/full_table	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
diff -r 41030a6c03b7 -r bb935709506a test-data/proteome_results/missing_buscos_list
--- a/test-data/proteome_results/missing_buscos_list	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/proteome_results/missing_buscos_list	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
diff -r 41030a6c03b7 -r bb935709506a test-data/proteome_results/short_summary
--- a/test-data/proteome_results/short_summary	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/proteome_results/short_summary	Thu Jan 12 13:28:58 2023 +0000
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmpctznxi43/files/8/5/3/dataset_853c93b4-f61b-4a14-a96c-ade0e2f5bbbd.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_6.dat
 # BUSCO was run in mode: proteins
 
 	***** Results: *****
@@ -15,3 +15,4 @@
 
 Dependencies and versions:
 	hmmsearch: 3.1
+	busco: 5.4.4
diff -r 41030a6c03b7 -r bb935709506a test-data/proteome_results/summary.png
Binary file test-data/proteome_results/summary.png has changed
diff -r 41030a6c03b7 -r bb935709506a test-data/transcriptome_results/full_table
--- a/test-data/transcriptome_results/full_table	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/transcriptome_results/full_table	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
diff -r 41030a6c03b7 -r bb935709506a test-data/transcriptome_results/missing_buscos_list
--- a/test-data/transcriptome_results/missing_buscos_list	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/transcriptome_results/missing_buscos_list	Thu Jan 12 13:28:58 2023 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
diff -r 41030a6c03b7 -r bb935709506a test-data/transcriptome_results/out.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transcriptome_results/out.gff	Thu Jan 12 13:28:58 2023 +0000
@@ -0,0 +1,5 @@
+##gff-version 3
+BUSCOaEOG7B0HST	MetaEuk	gene	1	2700	1493	+	.	Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0
+BUSCOaEOG7B0HST	MetaEuk	mRNA	1	2700	1493	+	.	Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_mRNA;Parent=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0
+BUSCOaEOG7B0HST	MetaEuk	exon	1	2700	1493	+	.	Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_exon_0;Parent=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_mRNA
+BUSCOaEOG7B0HST	MetaEuk	CDS	1	2700	1493	+	.	Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_CDS_0;Parent=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_exon_0
diff -r 41030a6c03b7 -r bb935709506a test-data/transcriptome_results/short_summary
--- a/test-data/transcriptome_results/short_summary	Mon Apr 11 09:02:11 2022 +0000
+++ b/test-data/transcriptome_results/short_summary	Thu Jan 12 13:28:58 2023 +0000
@@ -1,7 +1,7 @@
-# BUSCO version is: 5.2.1 
+# BUSCO version is: 5.4.4 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmpctznxi43/files/b/5/f/dataset_b5fc3813-7cbb-4aa0-b30c-dc2a6e85905d.dat
-# BUSCO was run in mode: transcriptome
+# Summarized benchmarking in BUSCO notation for file /tmp/tmprqvmp912/files/000/dataset_12.dat
+# BUSCO was run in mode: euk_tran
 
 	***** Results: *****
 
@@ -15,4 +15,5 @@
 
 Dependencies and versions:
 	hmmsearch: 3.1
-	metaeuk: 4.a0f584d
+	metaeuk: 6.a5d39d9
+	busco: 5.4.4
diff -r 41030a6c03b7 -r bb935709506a test-data/transcriptome_results/summary.png
Binary file test-data/transcriptome_results/summary.png has changed