Repository 'busco'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/busco

Changeset 19:2a5b8b9936bf (2023-11-14)
Previous changeset 18:94170eee0ad8 (2023-04-14) Next changeset 20:ea8146ee148f (2024-03-18)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
modified:
busco.xml
macros.xml
test-data/genome_results/full_table
test-data/genome_results/full_table_cached
test-data/genome_results/missing_buscos_list
test-data/genome_results/short_summary
test-data/genome_results/short_summary_cached
test-data/genome_results_metaeuk/full_table
test-data/genome_results_metaeuk/missing_buscos_list
test-data/genome_results_metaeuk/short_summary
test-data/genome_results_metaeuk/summary.png
test-data/genome_results_metaeuk_auto/full_table
test-data/genome_results_metaeuk_auto/missing_buscos_list
test-data/genome_results_metaeuk_auto/short_summary
test-data/genome_results_metaeuk_auto/summary.png
test-data/proteome_results/full_table
test-data/proteome_results/missing_buscos_list
test-data/proteome_results/short_summary
test-data/proteome_results/summary.png
test-data/transcriptome_results/full_table
test-data/transcriptome_results/missing_buscos_list
test-data/transcriptome_results/short_summary
test-data/transcriptome_results/summary.png
added:
test-data/genome_results/miniprot_1000.gff
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf busco.xml
--- a/busco.xml Fri Apr 14 08:13:46 2023 +0000
+++ b/busco.xml Tue Nov 14 13:03:37 2023 +0000
[
@@ -35,6 +35,7 @@
 --cpu \${GALAXY_SLOTS:-4}
 --evalue ${adv.evalue}
 --limit ${adv.limit}
+--contig_break ${adv.contig_break}
 
 #if $lineage_conditional.selector == 'cached':
     --offline
@@ -48,6 +49,7 @@
 #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':
 
     ${busco_mode.use_augustus.long}
@@ -60,6 +62,12 @@
     #end if
 #end if
 
+#if str( $busco_mode.mode ) == "geno":
+    #if $busco_mode.miniprot:
+        --miniprot
+    #end if
+#end if
+    
 #if $outputs and 'image' in $outputs:
     &&
     mkdir BUSCO_summaries
@@ -78,6 +86,7 @@
     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." />
@@ -102,6 +111,7 @@
                 <option value="prot">annotated gene sets (protein)</option>
             </param>
             <when value="geno">
+                <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/>
                 <conditional name="use_augustus">
                     <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
                         <option value="yes">Yes, use Augustus</option>
@@ -162,8 +172,10 @@
         <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 argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
         </section>
     </inputs>
+
     <outputs>
         <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
             <filter>outputs and 'short_summary' in outputs</filter>
@@ -178,7 +190,11 @@
         <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
             <filter>outputs and 'gff' in outputs</filter>
         </data>
+        <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff">
+            <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter>
+        </data>               
     </outputs>
+    
     <tests>
         <test expect_num_outputs="4">
             <param name="input" value="genome.fa" />
@@ -244,7 +260,7 @@
             <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="3">
+        <test expect_num_outputs="4">
             <param name="input" value="genome.fa" />
             <conditional name="lineage">
                 <param name="lineage_mode" value="select_lineage" />
@@ -252,6 +268,7 @@
             </conditional>
             <conditional name="busco_mode">
                 <param name="mode" value="geno" />
+                <param name="miniprot" value="true"/>
                 <conditional name="use_augustus">
                     <param name="use_augustus_selector" value="yes" />
                     <conditional name="aug_prediction">
@@ -269,6 +286,8 @@
                     <has_text text="##gff-version 3" />
                 </assert_contents>
             </output>
+            <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. -->
+            <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/>
         </test>
         <test expect_num_outputs="3">
             <param name="input" value="genome.fa" />
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf macros.xml
--- a/macros.xml Fri Apr 14 08:13:46 2023 +0000
+++ b/macros.xml Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">5.4.6</token>
+    <token name="@TOOL_VERSION@">5.5.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="citations">
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/full_table
--- a/test-data/genome_results/full_table Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results/full_table Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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
@@ -509,7 +509,7 @@
 93535at6656 Missing
 93797at6656 Missing
 94054at6656 Missing
-94238at6656 Complete sample 34764 38486 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1
+94238at6656 Complete sample:34764-38486 34764 38486 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1
 94263at6656 Missing
 94304at6656 Missing
 94473at6656 Missing
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/full_table_cached
--- a/test-data/genome_results/full_table_cached Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results/full_table_cached Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.6 
+# BUSCO version is: 5.5.0 
 # The lineage dataset is: archaea_odb10 (Creation date: 2021-02-23, number of genomes: 404, number of BUSCOs: 194)
 # Busco id Status Sequence Gene Start Gene End Strand Score Length
 860at2157 Missing
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/miniprot_1000.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results/miniprot_1000.gff Tue Nov 14 13:03:37 2023 +0000
b
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b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/missing_buscos_list
--- a/test-data/genome_results/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/short_summary
--- a/test-data/genome_results/short_summary Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results/short_summary Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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/tmprqvmp912/files/000/dataset_22.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpbmq1q2c6/files/8/e/b/dataset_8eb218b1-f367-4315-9915-554c009808cb.dat
 # BUSCO was run in mode: euk_genome_aug
 # Gene predictor used: augustus
 
@@ -26,10 +26,10 @@
 Dependencies and versions:
  hmmsearch: 3.1
  bbtools: 39.01
- makeblastdb: 2.13.0+
- tblastn: 2.13.0+
+ makeblastdb: 2.14.0+
+ tblastn: 2.14.0+
  augustus: 3.5.0
  gff2gbSmallDNA.pl: None
  new_species.pl: None
  etraining: None
- busco: 5.4.4
+ busco: 5.5.0
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results/short_summary_cached
--- a/test-data/genome_results/short_summary_cached Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results/short_summary_cached Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.4.6 
+# BUSCO version is: 5.5.0 
 # The lineage dataset is: archaea_odb10 (Creation date: 2021-02-23, number of genomes: 404, number of BUSCOs: 194)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmpte_du6dt/files/000/dataset_1.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpbmq1q2c6/files/3/3/0/dataset_330f49ed-7a6b-4380-870f-22494bb4b257.dat
 # BUSCO was run in mode: prok_genome
 # Gene predictor used: prodigal
 
@@ -27,4 +27,4 @@
  hmmsearch: 3.1
  bbtools: 39.01
  prodigal: 2.6.3
- busco: 5.4.6
+ busco: 5.5.0
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk/full_table
--- a/test-data/genome_results_metaeuk/full_table Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results_metaeuk/full_table Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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
@@ -340,7 +340,7 @@
 68939at6656 Missing
 68961at6656 Missing
 68981at6656 Missing
-68987at6656 Complete sample 40255 42070 + 122.8 266 https://www.orthodb.org/v10?query=68987at6656 mannose-1-phosphate guanyltransferase alpha
+68987at6656 Complete sample:40255-42070 40255 42070 + 122.8 266 https://www.orthodb.org/v10?query=68987at6656 mannose-1-phosphate guanyltransferase alpha
 69201at6656 Missing
 69238at6656 Missing
 69284at6656 Missing
@@ -509,7 +509,7 @@
 93535at6656 Missing
 93797at6656 Missing
 94054at6656 Missing
-94238at6656 Complete sample 34845 35678 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1
+94238at6656 Complete sample:35678-34845 34845 35678 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1
 94263at6656 Missing
 94304at6656 Missing
 94473at6656 Missing
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk/missing_buscos_list
--- a/test-data/genome_results_metaeuk/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results_metaeuk/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk/short_summary
--- a/test-data/genome_results_metaeuk/short_summary Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results_metaeuk/short_summary Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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/tmprqvmp912/files/000/dataset_28.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/1/d/2/dataset_1d20a949-adce-4511-8cab-345d59a61a05.dat
 # BUSCO was run in mode: euk_genome_met
 # Gene predictor used: metaeuk
 
@@ -27,4 +27,4 @@
  hmmsearch: 3.1
  bbtools: 39.01
  metaeuk: 6.a5d39d9
- busco: 5.4.4
+ busco: 5.5.0
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk/summary.png
b
Binary file test-data/genome_results_metaeuk/summary.png has changed
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk_auto/full_table
--- a/test-data/genome_results_metaeuk_auto/full_table Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results_metaeuk_auto/full_table Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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
@@ -131,7 +131,7 @@
 1041560at2759 Missing
 1049599at2759 Missing
 1051021at2759 Missing
-1053181at2759 Complete sample 34845 35678 - 45.0 149
+1053181at2759 Complete sample:35678-34845 34845 35678 - 45.0 149
 1057950at2759 Missing
 1065019at2759 Missing
 1076134at2759 Missing
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk_auto/missing_buscos_list
--- a/test-data/genome_results_metaeuk_auto/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results_metaeuk_auto/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255)
 # Busco id
 1001705at2759
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk_auto/short_summary
--- a/test-data/genome_results_metaeuk_auto/short_summary Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/genome_results_metaeuk_auto/short_summary Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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/tmprqvmp912/files/000/dataset_34.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/a/5/a/dataset_a5adf25d-f667-41d6-9472-f8661403e128.dat
 # BUSCO was run in mode: euk_genome_met
 # Gene predictor used: metaeuk
 
@@ -27,5 +27,5 @@
  hmmsearch: 3.1
  bbtools: 39.01
  prodigal: 2.6.3
- busco: 5.4.4
+ busco: 5.5.0
  metaeuk: 6.a5d39d9
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/genome_results_metaeuk_auto/summary.png
b
Binary file test-data/genome_results_metaeuk_auto/summary.png has changed
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/proteome_results/full_table
--- a/test-data/proteome_results/full_table Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/proteome_results/full_table Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/proteome_results/missing_buscos_list
--- a/test-data/proteome_results/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/proteome_results/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/proteome_results/short_summary
--- a/test-data/proteome_results/short_summary Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/proteome_results/short_summary Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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/tmprqvmp912/files/000/dataset_6.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/b/a/7/dataset_ba764d57-9365-4d54-a1f8-ac1350df0747.dat
 # BUSCO was run in mode: proteins
 
  ***** Results: *****
@@ -15,4 +15,4 @@
 
 Dependencies and versions:
  hmmsearch: 3.1
- busco: 5.4.4
+ busco: 5.5.0
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/proteome_results/summary.png
b
Binary file test-data/proteome_results/summary.png has changed
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/transcriptome_results/full_table
--- a/test-data/transcriptome_results/full_table Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/transcriptome_results/full_table Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/transcriptome_results/missing_buscos_list
--- a/test-data/transcriptome_results/missing_buscos_list Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/transcriptome_results/missing_buscos_list Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,4 +1,4 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/transcriptome_results/short_summary
--- a/test-data/transcriptome_results/short_summary Fri Apr 14 08:13:46 2023 +0000
+++ b/test-data/transcriptome_results/short_summary Tue Nov 14 13:03:37 2023 +0000
b
@@ -1,6 +1,6 @@
-# BUSCO version is: 5.4.4 
+# BUSCO version is: 5.5.0 
 # 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/tmprqvmp912/files/000/dataset_12.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/4/3/b/dataset_43bb7c5f-29dc-4638-a19d-abb98c145794.dat
 # BUSCO was run in mode: euk_tran
 
  ***** Results: *****
@@ -16,4 +16,4 @@
 Dependencies and versions:
  hmmsearch: 3.1
  metaeuk: 6.a5d39d9
- busco: 5.4.4
+ busco: 5.5.0
b
diff -r 94170eee0ad8 -r 2a5b8b9936bf test-data/transcriptome_results/summary.png
b
Binary file test-data/transcriptome_results/summary.png has changed