# HG changeset patch
# User iuc
# Date 1759600087 0
# Node ID c5a90fa4b8dd10444fe5e9ebe140081158c833b4
# Parent 4e70d88adf2f8ef84de230290d6c194e7dfac756
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 1696bfc7f5bade0686ad6731da06a436c43b59e5
diff -r 4e70d88adf2f -r c5a90fa4b8dd busco.xml
--- a/busco.xml Fri Apr 04 11:18:42 2025 +0000
+++ b/busco.xml Sat Oct 04 17:48:07 2025 +0000
@@ -25,9 +25,9 @@
## - download complete reference DB (~200G, final 105G) to tools/busco/test-data/test-db/busco_downloads
## ```
## busco --download_path tools/busco/test-data/test-db/busco_downloads/ --download all
-## find tools/busco/test-data/test-db/busco_downloads/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -exec rm -rf {} \;
-## find tools/busco/test-data/test-db/busco_downloads/placement_files -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -delete
-## find tools/busco/test-data/test-db/busco_downloads/lineages/ -name "*.faa.gz" -exec gunzip {} \;;
+## find tools/busco/test-data/busco_downloads/lineages/ -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -exec rm -rf {} \;
+## find tools/busco/test-data/busco_downloads/placement_files -mindepth 1 -maxdepth 1 ! -name '*_odb10*' -delete
+## find tools/busco/test-data/busco_downloads/lineages/ -name "*.faa.gz" -exec gunzip {} \;;
## ```
## - test containerized (note: test-data is mounted ro in containerized tests)
##
@@ -96,22 +96,66 @@
#end if
#end if
-#if $outputs and 'image' in $outputs:
- && mkdir BUSCO_summaries
- && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
- && generate_plot.py -wd BUSCO_summaries -rt specific
+#if $lineage.lineage_mode != "auto_detect":
+ && cp busco_galaxy/run_*/full_table.tsv busco_galaxy/full_table_specific_lineage.tsv
+ && cp busco_galaxy/run_*/missing_busco_list.tsv busco_galaxy/missing_busco_list_specific_lineage.tsv
+ #if $outputs and 'image' in $outputs:
+ && mkdir BUSCO_summaries
+ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
+ && generate_plot.py -wd BUSCO_summaries -rt specific
+ && cp BUSCO_summaries/busco_figure.png busco_galaxy/busco_figure_specific_lineage.png
+ #end if
+
+ #if $outputs and 'gff' in $outputs:
+ && echo "\##gff-version 3" > busco_galaxy/busco_output.gff
+ ## gff files can be absent
+ && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_specific.gff 2> /dev/null || true)
+ #end if
+ #if $outputs and 'faa' in $outputs:
+ && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.faa >> busco_galaxy/busco_output_specific.faa 2> /dev/null || true)
+ #end if
+ #if $outputs and 'fna' in $outputs:
+ && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.fna >> busco_galaxy/busco_output_specific.fna 2> /dev/null || true)
+ #end if
#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
-#if $outputs and 'faa' in $outputs:
- && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.faa >> busco_output.faa 2> /dev/null || true)
-#end if
-#if $outputs and 'fna' in $outputs:
- && (cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.fna >> busco_output.fna 2> /dev/null || true)
+## if $lineage.lineage_mode == "auto_detect", BUSCO output several files with the same name, causing an issue, we need to rename the files
+#if $lineage.lineage_mode == "auto_detect":
+ && specific_lineage=\$(find ./busco_galaxy -name "short_summary.specific.*.txt" | head -n 1 | cut -d'.' -f4)
+ && generic_lineage=\$(find ./busco_galaxy -name "short_summary.generic.*.txt" | head -n 1 | cut -d'.' -f4)
+
+ ##Rename the output files to differenciate specific and generic lineages results
+ ## Full table
+ && cp busco_galaxy/run_\${specific_lineage}/full_table.tsv busco_galaxy/full_table_specific_lineage.tsv
+ && cp busco_galaxy/run_\${generic_lineage}/full_table.tsv busco_galaxy/full_table_generic_lineage.tsv
+ ##Missing busco list
+ && cp busco_galaxy/run_\${specific_lineage}/missing_busco_list.tsv busco_galaxy/missing_busco_list_specific_lineage.tsv
+ && cp busco_galaxy/run_\${generic_lineage}/missing_busco_list.tsv busco_galaxy/missing_busco_list_generic_lineage.tsv
+ #if $outputs and 'image' in $outputs:
+ && mkdir BUSCO_summaries_specific
+ && cp busco_galaxy/short_summary.specific.*.txt BUSCO_summaries_specific/
+ && generate_plot.py -wd BUSCO_summaries_specific -rt specific
+ && cp BUSCO_summaries_specific/busco_figure.png busco_galaxy/busco_figure_specific_lineage.png
+ && mkdir BUSCO_summaries_generic
+ && cp busco_galaxy/short_summary.generic.*.txt BUSCO_summaries_generic/
+ && generate_plot.py -wd BUSCO_summaries_generic -rt generic
+ && cp BUSCO_summaries_generic/busco_figure.png busco_galaxy/busco_figure_generic_lineage.png
+ #end if
+ #if $outputs and 'gff' in $outputs:
+ ## gff files can be absent
+ && echo "\##gff-version 3" > busco_galaxy/busco_output_specific.gff
+ && (cat busco_galaxy/run_\${specific_lineage}/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_specific.gff 2> /dev/null || true)
+ && echo "\##gff-version 3" > busco_galaxy/busco_output_generic.gff
+ && (cat busco_galaxy/run_\${generic_lineage}/busco_sequences/*busco_sequences/*.gff >> busco_galaxy/busco_output_generic.gff 2> /dev/null || true)
+ #end if
+ #if $outputs and 'faa' in $outputs:
+ && (cat busco_galaxy/run_\${specific_lineage}/busco_sequences/*busco_sequences/*.faa >> busco_galaxy/busco_output_specific.faa 2> /dev/null || true)
+ && (cat busco_galaxy/run_\${generic_lineage}/busco_sequences/*busco_sequences/*.faa >> busco_galaxy/busco_output_generic.faa 2> /dev/null || true)
+ #end if
+ #if $outputs and 'fna' in $outputs:
+ && (cat busco_galaxy/run_\${specific_lineage}/busco_sequences/*busco_sequences/*.fna >> busco_galaxy/busco_output_specific.fna 2> /dev/null || true)
+ && (cat busco_galaxy/run_\${generic_lineage}/busco_sequences/*busco_sequences/*.fna >> busco_galaxy/busco_output_generic.fna 2> /dev/null || true)
+ #end if
#end if
]]>
@@ -172,6 +216,7 @@
+
@@ -183,9 +228,9 @@
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@@ -199,26 +244,49 @@
-
+
outputs and 'short_summary' in outputs
-
-
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+ (outputs and 'short_summary' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']
+
+
+
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+ lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']
+
+
outputs and 'missing' in outputs
-
+
+ (outputs and 'missing' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']
+
+
outputs and 'image' in outputs
-
+
+ (outputs and 'image' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']
+
+
outputs and 'gff' in outputs
-
+
+ (outputs and 'gff' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']
+
+
outputs and 'faa' in outputs
-
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+ (outputs and 'faa' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']
+
+
outputs and 'fna' in outputs
+
+
+ (outputs and 'fna' in outputs) and lineage['lineage_mode'] == 'auto_detect' and lineage['generic_results']
+
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@@ -434,23 +526,50 @@
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-