# HG changeset patch # User iuc # Date 1508486075 14400 # Node ID 382a4c19007f085ea01e500b2637a514623f5f20 # Parent 87983967544bf31c26784bff8b2f1c3e513a11bb planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e diff -r 87983967544b -r 382a4c19007f busco.xml --- a/busco.xml Tue Jan 24 12:08:38 2017 -0500 +++ b/busco.xml Fri Oct 20 03:54:35 2017 -0400 @@ -1,22 +1,39 @@ - + assess genome assembly and annotation completeness - - busco + busco + r-ggplot2 + /dev/null && + + export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && + #end if + + run_BUSCO.py --in '${input}' - --lineage '${lineage.fields.path}' + --lineage_path '${lineage_path.fields.path}/${lineage_path.fields.value}' --mode '${mode}' -o "busco_galaxy" --cpu \${GALAXY_SLOTS:-4} --evalue ${adv.evalue} ${adv.long} --limit ${adv.limit} - #if $adv.species: - --species '${adv.species}' + #if $adv.aug_prediction.augustus_mode == 'builtin': + --species '${adv.aug_prediction.augustus_species}' + #else if $adv.aug_prediction.augustus_mode == 'history': + --species local #end if --tarzip ]]> @@ -24,14 +41,13 @@ - - + @@ -41,7 +57,118 @@

- + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

@@ -53,7 +180,7 @@ - + @@ -61,7 +188,7 @@ - + @@ -69,12 +196,32 @@ - + + + + + + + + + + + + + + + + + + + + + BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs diff -r 87983967544b -r 382a4c19007f test-data/busco.loc --- a/test-data/busco.loc Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/busco.loc Fri Oct 20 03:54:35 2017 -0400 @@ -1,1 +1,1 @@ -arthropoda_2.0 arthropoda_2.0 Arthropoda (v2) ${__HERE__}/arthropoda/ +arthropoda Arthropoda data ${__HERE__}/ diff -r 87983967544b -r 382a4c19007f test-data/genome_results/full_table --- a/test-data/genome_results/full_table Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/genome_results/full_table Fri Oct 20 03:54:35 2017 -0400 @@ -1,5 +1,5 @@ -# BUSCO version is: 2.0 -# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# BUSCO version is: 3.0.2 +# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) # To reproduce this run: python /tmp/tmpeQaU9k/job_working_directory/000/2/conda-env/bin/BUSCO.py -i /tmp/tmpeQaU9k/files/000/dataset_1.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m genome -c 1 -sp generic -e 0.01 -z # # Busco id Status Contig Start End Score Length diff -r 87983967544b -r 382a4c19007f test-data/genome_results/missing_buscos_list --- a/test-data/genome_results/missing_buscos_list Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/genome_results/missing_buscos_list Fri Oct 20 03:54:35 2017 -0400 @@ -1,5 +1,5 @@ -# BUSCO version is: 2.0 -# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# BUSCO version is: 3.0.2 +# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) # To reproduce this run: python /tmp/tmpeQaU9k/job_working_directory/000/2/conda-env/bin/BUSCO.py -i /tmp/tmpeQaU9k/files/000/dataset_1.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m genome -c 1 -sp generic -e 0.01 -z # BUSCOaEOG7B0HST diff -r 87983967544b -r 382a4c19007f test-data/genome_results/short_summary --- a/test-data/genome_results/short_summary Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/genome_results/short_summary Fri Oct 20 03:54:35 2017 -0400 @@ -1,5 +1,5 @@ -# BUSCO version is: 2.0 -# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# BUSCO version is: 3.0.2 +# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) # To reproduce this run: python /tmp/tmpeQaU9k/job_working_directory/000/2/conda-env/bin/BUSCO.py -i /tmp/tmpeQaU9k/files/000/dataset_1.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m genome -c 1 -sp generic -e 0.01 -z # # Summarized benchmarking in BUSCO notation for file /tmp/tmpeQaU9k/files/000/dataset_1.dat diff -r 87983967544b -r 382a4c19007f test-data/local.tar.gz Binary file test-data/local.tar.gz has changed diff -r 87983967544b -r 382a4c19007f test-data/proteome_results/full_table --- a/test-data/proteome_results/full_table Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/proteome_results/full_table Fri Oct 20 03:54:35 2017 -0400 @@ -1,5 +1,5 @@ -# BUSCO version is: 2.0 -# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# BUSCO version is: 3.0.2 +# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) # To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/4/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_5.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m proteins -c 1 -sp generic -e 0.01 -z # # Busco id Status Sequence Score Length diff -r 87983967544b -r 382a4c19007f test-data/proteome_results/missing_buscos_list --- a/test-data/proteome_results/missing_buscos_list Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/proteome_results/missing_buscos_list Fri Oct 20 03:54:35 2017 -0400 @@ -1,4 +1,4 @@ -# BUSCO version is: 2.0 -# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# BUSCO version is: 3.0.2 +# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) # To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/4/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_5.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m proteins -c 1 -sp generic -e 0.01 -z # diff -r 87983967544b -r 382a4c19007f test-data/proteome_results/short_summary --- a/test-data/proteome_results/short_summary Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/proteome_results/short_summary Fri Oct 20 03:54:35 2017 -0400 @@ -1,5 +1,5 @@ -# BUSCO version is: 2.0 -# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# BUSCO version is: 3.0.2 +# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) # To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/4/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_5.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m proteins -c 1 -sp generic -e 0.01 -z # # Summarized benchmarking in BUSCO notation for file /tmp/tmpCgx5rU/files/000/dataset_5.dat diff -r 87983967544b -r 382a4c19007f test-data/transcriptome_results/full_table --- a/test-data/transcriptome_results/full_table Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/transcriptome_results/full_table Fri Oct 20 03:54:35 2017 -0400 @@ -1,5 +1,5 @@ -# BUSCO version is: 2.0 -# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# BUSCO version is: 3.0.2 +# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) # To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/6/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_9.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m tran -c 1 -sp generic -e 0.01 -z # # Busco id Status Sequence Score Length diff -r 87983967544b -r 382a4c19007f test-data/transcriptome_results/missing_buscos_list --- a/test-data/transcriptome_results/missing_buscos_list Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/transcriptome_results/missing_buscos_list Fri Oct 20 03:54:35 2017 -0400 @@ -1,5 +1,5 @@ -# BUSCO version is: 2.0 -# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# BUSCO version is: 3.0.2 +# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) # To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/6/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_9.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m tran -c 1 -sp generic -e 0.01 -z # BUSCOaEOG7B0HST diff -r 87983967544b -r 382a4c19007f test-data/transcriptome_results/short_summary --- a/test-data/transcriptome_results/short_summary Tue Jan 24 12:08:38 2017 -0500 +++ b/test-data/transcriptome_results/short_summary Fri Oct 20 03:54:35 2017 -0400 @@ -1,9 +1,9 @@ -# BUSCO version is: 2.0 -# The lineage dataset is: arthropoda (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) +# BUSCO version is: 3.0.2 +# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A) # To reproduce this run: python /tmp/tmpCgx5rU/job_working_directory/000/6/conda-env/bin/BUSCO.py -i /tmp/tmpCgx5rU/files/000/dataset_9.dat -o busco_galaxy -l /home/abretaud/iuc_tools_abretaud/tools/busco/test-data/arthropoda/ -m tran -c 1 -sp generic -e 0.01 -z # # Summarized benchmarking in BUSCO notation for file /tmp/tmpCgx5rU/files/000/dataset_9.dat -# BUSCO was run in mode: tran +# BUSCO was run in mode: transcriptome C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:1 diff -r 87983967544b -r 382a4c19007f tool-data/busco.loc.sample --- a/tool-data/busco.loc.sample Tue Jan 24 12:08:38 2017 -0500 +++ b/tool-data/busco.loc.sample Fri Oct 20 03:54:35 2017 -0400 @@ -1,13 +1,13 @@ # This is a sample file distributed with Galaxy that is used to define a # list of busco datasets, using four columns tab separated: # -# +# # # Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html # # "/some/path/arthropoda/" would be the last column in the line # If this were for the mm10 mouse genome, the resulting entry would look like: # -#arthropoda_2.0 arthropoda_2.0 Arthropoda (v2) /some/path/arthropoda/ +#arthropoda_2.0 arthropoda_2.0 /some/path/arthropoda/ # # diff -r 87983967544b -r 382a4c19007f tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Jan 24 12:08:38 2017 -0500 +++ b/tool_data_table_conf.xml.sample Fri Oct 20 03:54:35 2017 -0400 @@ -1,6 +1,6 @@ - value, dbkey, name, path + value, name, path

diff -r 87983967544b -r 382a4c19007f tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Tue Jan 24 12:08:38 2017 -0500 +++ b/tool_data_table_conf.xml.test Fri Oct 20 03:54:35 2017 -0400 @@ -1,6 +1,6 @@ - value, dbkey, name, path + value, name, path