| Previous changeset 6:1e62c28ba91d (2019-12-04) Next changeset 8:602fb8e63aa7 (2020-12-30) |
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Commit message:
"planemo upload commit 22186dcfbe33d17fabd4a3c4fa39d4313978fc9c" |
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modified:
busco.xml test-data/genome.fa test-data/genome_results/full_table test-data/genome_results/missing_buscos_list test-data/genome_results/short_summary test-data/proteome_results/full_table test-data/proteome_results/missing_buscos_list test-data/proteome_results/short_summary test-data/transcriptome_results/full_table test-data/transcriptome_results/missing_buscos_list test-data/transcriptome_results/short_summary |
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added:
macros.xml |
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removed:
test-data/arthropoda/ancestral test-data/arthropoda/clade_parameters test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm test-data/arthropoda/lengths_cutoff test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl test-data/arthropoda/scores_cutoff test-data/busco.loc tool-data/busco.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 1e62c28ba91d -r 4048d82f0c88 busco.xml --- a/busco.xml Wed Dec 04 13:45:35 2019 -0500 +++ b/busco.xml Mon Aug 17 06:50:18 2020 -0400 |
| [ |
| b'@@ -1,17 +1,14 @@\n-<tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@+galaxy2">\n+<tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@">\n <description>assess genome assembly and annotation completeness</description>\n <macros>\n- <token name="@TOOL_VERSION@">3.0.2</token>\n+ <import>macros.xml</import>\n </macros>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">busco</requirement>\n- <requirement type="package" version="3.5.1">r-base</requirement>\n- <requirement type="package" version="3.3.2">augustus</requirement>\n- <requirement type="package" version="1.29">tar</requirement>\n+ <requirement type="package" version="1.32">tar</requirement>\n </requirements>\n <command><![CDATA[\n-export BUSCO_CONFIG_FILE=\'busco_config.ini\' &&\n-if [ -z "\\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\\$(dirname \\$(which run_BUSCO.py)) ; export AUGUSTUS_CONFIG_PATH=\\$(realpath \\${BUSCO_PATH}/../config) ; fi &&\n+if [ -z "\\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\\$(dirname \\$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\\$(realpath \\${BUSCO_PATH}/../config) ; fi &&\n cp -r "\\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&\n export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&\n \n@@ -21,9 +18,10 @@\n tar -C \'augustus_dir/species/\' -xzf \'${adv.aug_prediction.augustus_model}\' &&\n #end if\n \n-run_BUSCO.py\n+busco\n --in \'${input}\'\n---lineage_path \'${lineage_path.fields.path}/${lineage_path.fields.value}\'\n+--lineage_dataset \'${lineage_dataset}\'\n+--update-data\n --mode \'${mode}\'\n -o busco_galaxy\n --cpu \\${GALAXY_SLOTS:-4}\n@@ -31,11 +29,10 @@\n ${adv.long}\n --limit ${adv.limit}\n #if $adv.aug_prediction.augustus_mode == \'builtin\':\n- --species \'${adv.aug_prediction.augustus_species}\'\n+ --augustus_species \'${adv.aug_prediction.augustus_species}\'\n #else if $adv.aug_prediction.augustus_mode == \'history\':\n- --species local\n+ --augustus_species local\n #end if\n---tarzip\n ]]></command>\n \n <inputs>\n@@ -46,11 +43,8 @@\n <option value="prot">Proteome</option>\n </param>\n \n- <param argument="--lineage_path" type="select" label="Lineage">\n- <options from_data_table="busco">\n- <filter type="sort_by" column="2" />\n- <validator type="no_options" message="No indexes are available" />\n- </options>\n+ <param argument="--lineage_dataset" type="select" label="Lineage">\n+ <expand macro="lineages"/>\n </param>\n \n <section name="adv" title="Advanced Options" expanded="False">\n@@ -69,102 +63,7 @@\n </when>\n <when value="builtin">\n <param name="augustus_species" type="select" label="Augustus species model">\n- <!-- If you update this list, please also update it in maker and augustus tools (../maker/maker.xml and ../augustus/augustus.xml) -->\n- <option value="human">Homo sapiens</option>\n- <option value="fly">Drosophila melanogaster</option>\n- <option value="arabidopsis">Arabidopsis thaliana</option>\n- <option value="brugia ">Brugia malayi</option>\n- <option value="aedes">Aedes aegypti</option>\n- <option value="tribolium2012">Tribolium castaneum</option>\n- <option value="schistosoma">Schistosoma mansoni</option>\n- <option value="tetrahymena">Tetrahymena thermophila</option>\n- <option value="galdieria">Galdieria sulphuraria</option>\n- <option value="maize">Zea mays</option>\n- <option value="toxoplasma">Toxoplasma gondii</option>\n- <option value="caenorhabditis ">Caenorhabditis elegans</option>\n- <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>\n- '..b'option>\n- <option value="schistosoma2">schistosoma2</option>\n- <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>\n+ <expand macro="augustus_species"/>\n </param>\n </when>\n </conditional>\n@@ -172,14 +71,14 @@\n </section>\n </inputs>\n <outputs>\n- <data name=\'busco_sum\' format=\'txt\' label="${tool.name} on ${on_string}: short summary" from_work_dir="run_busco_galaxy/short_summary_busco_galaxy.txt"/>\n- <data name=\'busco_table\' format=\'tabular\' label="${tool.name} on ${on_string}: full table" from_work_dir="run_busco_galaxy/full_table_busco_galaxy.tsv"/>\n- <data name=\'busco_missing\' format=\'tabular\' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="run_busco_galaxy/missing_busco_list_busco_galaxy.tsv"/>\n+ <data name=\'busco_sum\' format=\'txt\' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"/>\n+ <data name=\'busco_table\' format=\'tabular\' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/>\n+ <data name=\'busco_missing\' format=\'tabular\' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv"/>\n </outputs>\n <tests>\n <test>\n <param name="input" value="genome.fa"/>\n- <param name="lineage_path" value="arthropoda"/>\n+ <param name="lineage_dataset" value="arthropoda_odb10"/>\n <param name="mode" value="geno"/>\n <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>\n <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>\n@@ -187,7 +86,7 @@\n </test>\n <test>\n <param name="input" value="proteome.fa"/>\n- <param name="lineage_path" value="arthropoda"/>\n+ <param name="lineage_dataset" value="arthropoda_odb10"/>\n <param name="mode" value="prot"/>\n <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>\n <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>\n@@ -195,7 +94,7 @@\n </test>\n <test>\n <param name="input" value="transcriptome.fa"/>\n- <param name="lineage_path" value="arthropoda"/>\n+ <param name="lineage_dataset" value="arthropoda_odb10"/>\n <param name="mode" value="tran"/>\n <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>\n <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>\n@@ -203,7 +102,7 @@\n </test>\n <test>\n <param name="input" value="genome.fa"/>\n- <param name="lineage_path" value="arthropoda"/>\n+ <param name="lineage_dataset" value="arthropoda_odb10"/>\n <param name="mode" value="geno"/>\n <param name="adv|aug_prediction|augustus_mode" value="builtin"/>\n <param name="adv|aug_prediction|augustus_species" value="human"/>\n@@ -213,7 +112,7 @@\n </test>\n <test>\n <param name="input" value="genome.fa"/>\n- <param name="lineage_path" value="arthropoda"/>\n+ <param name="lineage_dataset" value="arthropoda_odb10"/>\n <param name="mode" value="geno"/>\n <param name="adv|aug_prediction|augustus_mode" value="history"/>\n <param name="adv|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>\n@@ -227,7 +126,5 @@\n \n .. _BUSCO: http://busco.ezlab.org/\n </help>\n- <citations>\n- <citation type="doi">doi:10.1093/bioinformatics/btv351</citation>\n- </citations>\n+ <expand macro="citations"/>\n </tool>\n' |
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| diff -r 1e62c28ba91d -r 4048d82f0c88 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Aug 17 06:50:18 2020 -0400 |
| b |
| b'@@ -0,0 +1,278 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@TOOL_VERSION@">4.1.2</token>\n+\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btv351</citation>\n+ </citations>\n+ </xml>\n+\n+ <xml name="augustus_species">\n+ <!-- If you update this list, please also update it in maker and augustus tools (../maker/maker.xml and ../augustus/augustus.xml) -->\n+ <option value="human">Homo sapiens</option>\n+ <option value="fly">Drosophila melanogaster</option>\n+ <option value="arabidopsis">Arabidopsis thaliana</option>\n+ <option value="brugia ">Brugia malayi</option>\n+ <option value="aedes">Aedes aegypti</option>\n+ <option value="tribolium2012">Tribolium castaneum</option>\n+ <option value="schistosoma">Schistosoma mansoni</option>\n+ <option value="tetrahymena">Tetrahymena thermophila</option>\n+ <option value="galdieria">Galdieria sulphuraria</option>\n+ <option value="maize">Zea mays</option>\n+ <option value="toxoplasma">Toxoplasma gondii</option>\n+ <option value="caenorhabditis ">Caenorhabditis elegans</option>\n+ <option value="aspergillus_fumigatus">Aspergillus fumigatus</option>\n+ <option value="aspergillus_nidulans ">Aspergillus nidulans</option>\n+ <option value="aspergillus_oryzae ">Aspergillus oryzae</option>\n+ <option value="aspergillus_terreus">Aspergillus terreus</option>\n+ <option value="botrytis_cinerea ">Botrytis cinerea</option>\n+ <option value="candida_albicans ">Candida albicans</option>\n+ <option value="candida_guilliermondii ">Candida guilliermondii</option>\n+ <option value="candida_tropicalis ">Candida tropicalis</option>\n+ <option value="chaetomium_globosum">Chaetomium globosum</option>\n+ <option value="coccidioides_immitis">Coccidioides immitis</option>\n+ <option value="coprinus">Coprinus cinereus</option>\n+ <option value="coprinus_cinereus">Coprinus cinereus</option>\n+ <option value="cryptococcus_neoformans_gattii">Cryptococcus neoformans gattii</option>\n+ <option value="cryptococcus_neoformans_neoformans_B">Cryptococcus neoformans neoformans</option>\n+ <option value="cryptococcus_neoformans_neoformans_JEC21">Cryptococcus neoformans neoformans</option>\n+ <option value="cryptococcus">Cryptococcus neoformans</option>\n+ <option value="debaryomyces_hansenii">Debaryomyces hansenii</option>\n+ <option value="encephalitozoon_cuniculi_GB">Encephalitozoon cuniculi</option>\n+ <option value="eremothecium_gossypii">Eremothecium gossypii</option>\n+ <option value="fusarium_graminearum ">Fusarium graminearum</option>\n+ <option value="histoplasma_capsulatum ">Histoplasma capsulatum</option>\n+ <option value="histoplasma">Histoplasma capsulatum</option>\n+ <option value="kluyveromyces_lactis ">Kluyveromyces lactis</option>\n+ <option value="laccaria_bicolor ">Laccaria bicolor</option>\n+ <option value="lamprey">Petromyzon marinus</option>\n+ <option value="leishmania_tarentolae">Leishmania tarentolae</option>\n+ <option value="lodderomyces_elongisporus">Lodderomyces elongisporus</option>\n+ <option value="magnaporthe_grisea ">Magnaporthe grisea</option>\n+ <option value="neurospora_crassa">Neurospora crassa</option>\n+ <option value="phanerochaete_chrysosporium">Phanerochaete chrysosporium</option>\n+ <option value="pichia_stipitis">Pichia stipitis</option>\n+ <option value="rhizopus_oryzae">Rhizopus oryzae</option>\n+ <option value="saccharomyces_cerevisiae_S288C">Saccharomyces cerevisiae</option>\n+ <option value="saccharomyces_cerevisiae_rm11-1a_1">Saccharomyces cerevisiae</option>\n+ <option value="saccharomyces">Saccharomyces cerevisiae</option>\n+ <option value="schizosaccharomyces_pombe">Schizosaccharomyces pombe</option>\n+ '..b'coplasmatales_odb10">Mycoplasmatales</option>\n+ <option value="natrialbales_odb10">Natrialbales</option>\n+ <option value="neisseriales_odb10">Neisseriales</option>\n+ <option value="nematoda_odb10">Nematoda</option>\n+ <option value="nitrosomonadales_odb10">Nitrosomonadales</option>\n+ <option value="nostocales_odb10">Nostocales</option>\n+ <option value="oceanospirillales_odb10">Oceanospirillales</option>\n+ <option value="onygenales_odb10">Onygenales</option>\n+ <option value="oscillatoriales_odb10">Oscillatoriales</option>\n+ <option value="passeriformes_odb10">Passeriformes</option>\n+ <option value="pasteurellales_odb10">Pasteurellales</option>\n+ <option value="planctomycetes_odb10">Planctomycetes</option>\n+ <option value="plasmodium_odb10">Plasmodium</option>\n+ <option value="pleosporales_odb10">Pleosporales</option>\n+ <option value="poales_odb10">Poales</option>\n+ <option value="polyporales_odb10">Polyporales</option>\n+ <option value="primates_odb10">Primates</option>\n+ <option value="propionibacteriales_odb10">Propionibacteriales</option>\n+ <option value="proteobacteria_odb10">Proteobacteria</option>\n+ <option value="pseudomonadales_odb10">Pseudomonadales</option>\n+ <option value="rhizobiales_odb10">Rhizobiales</option>\n+ <option value="rhizobium-agrobacterium_group_odb10">Rhizobium-agrobacterium group</option>\n+ <option value="rhodobacterales_odb10">Rhodobacterales</option>\n+ <option value="rhodospirillales_odb10">Rhodospirillales</option>\n+ <option value="rickettsiales_odb10">Rickettsiales</option>\n+ <option value="saccharomycetes_odb10">Saccharomycetes</option>\n+ <option value="sauropsida_odb10">Sauropsida</option>\n+ <option value="selenomonadales_odb10">Selenomonadales</option>\n+ <option value="solanales_odb10">Solanales</option>\n+ <option value="sordariomycetes_odb10">Sordariomycetes</option>\n+ <option value="sphingobacteriia_odb10">Sphingobacteriia</option>\n+ <option value="sphingomonadales_odb10">Sphingomonadales</option>\n+ <option value="spirochaetales_odb10">Spirochaetales</option>\n+ <option value="spirochaetes_odb10">Spirochaetes</option>\n+ <option value="spirochaetia_odb10">Spirochaetia</option>\n+ <option value="stramenopiles_odb10">Stramenopiles</option>\n+ <option value="streptomycetales_odb10">Streptomycetales</option>\n+ <option value="streptosporangiales_odb10">Streptosporangiales</option>\n+ <option value="sulfolobales_odb10">Sulfolobales</option>\n+ <option value="synechococcales_odb10">Synechococcales</option>\n+ <option value="synergistetes_odb10">Synergistetes</option>\n+ <option value="tenericutes_odb10">Tenericutes</option>\n+ <option value="tetrapoda_odb10">Tetrapoda</option>\n+ <option value="thaumarchaeota_odb10">Thaumarchaeota</option>\n+ <option value="thermoanaerobacterales_odb10">Thermoanaerobacterales</option>\n+ <option value="thermoplasmata_odb10">Thermoplasmata</option>\n+ <option value="thermoproteales_odb10">Thermoproteales</option>\n+ <option value="thermoprotei_odb10">Thermoprotei</option>\n+ <option value="thermotogae_odb10">Thermotogae</option>\n+ <option value="thiotrichales_odb10">Thiotrichales</option>\n+ <option value="tissierellales_odb10">Tissierellales</option>\n+ <option value="tissierellia_odb10">Tissierellia</option>\n+ <option value="tremellomycetes_odb10">Tremellomycetes</option>\n+ <option value="verrucomicrobia_odb10">Verrucomicrobia</option>\n+ <option value="vertebrata_odb10">Vertebrata</option>\n+ <option value="vibrionales_odb10">Vibrionales</option>\n+ <option value="viridiplantae_odb10">Viridiplantae</option>\n+ <option value="xanthomonadales_odb10">Xanthomonadales</option>\n+ </xml>\n+</macros>\n' |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/arthropoda/ancestral --- a/test-data/arthropoda/ancestral Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,20 +0,0 @@ ->BUSCOaEOG7B0HST -MAADQAQFQQLLVSLLSTDNEVRKQAEEAYNNLPVESKVTFLLGAIANGQLSEEVRQLAA -VLLRRLFSSEFLEFYKKLPAEAQAQLKEQILLAVQQEVSEQLRRKVCEVVAEVARNLIDE -DGNNQWPEFLQFLFQCANSPSPQLKESALRIFTSVPGIFGNQEAQYLDLIKQMLAKSLED -TEDAEVRLQAVRAVGAFILLHDKEKEIQKHFADLLPALLQVVAESIEKQDDDALLKVLID -LAEATPKFLRPQLETILELCLKVLSEEDVEDSWRHLALEVLVTLAETAPAMVRKRAEKYI -VALVPLVLKMMTDLEEDEDWSVADEITEDDNDSNNVVAESALDRLACGLGGKVVLPLVVE -AIPAMLSSSDWKKRHAALMAISAIGEGCHKQMEALLDQVLDGVLKYLQDPHPRVRYAACN -AIGQMSTDFAPIFEKKFHDKVIPGLLLLLDDEANPRVQAHAGAALVNFSEDCPKNILTRY -LDAIMAKLEAILTSKFKELVEKGTKLVLEQVVTTIASVADTAEEEFVAYYDRLMPCLKYI -IQNANSEELKLLRGKTIECVSLIGLAVGREKFIADASEVMDLLLKTHTEGAELPDDDPQT -SYLISAWARICKILGKQFEQYLPLVMGPVLRTASLKPEVALLDNEDLEDIEGDVDWQFVS -LGEQQNFGIRTAGLEDKASACEMLVCYARELKEGFAEYAEEVVRLMVPLLKFYFHDGVRT -AAAESLPYLLDCAKIKGPQYLEGMWAYICPELLKAIDTEPEKEVLSELLSSLAKCIETLG -AGCLSEEALKELLRILDKLLKEHFERAEKRLEKRKDEDYDEVVEEELAEEDDEDVYILSK -VADILHALFATYKEAFLPAFDQVVPHFVKLLEPERPLADRQWALCVFDDVIEFGGPACVK -YQEIFLRALLQYVSDKSAEVRQAAAYGCGVLGQFGGEQFAEACAEALPKLVEVINDPESR -ELENINATENAISAVTKILKYNKSAITNVDELLAVWLSWLPVVEDEEEAAHVYGYLCDLI -EANHPVVLGANNANLPRIVSILAEAFLREVVEAESAVAKRLLSIVKQIESNEELLQACIS -ELSAEQQQALKEALRELAA |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/arthropoda/clade_parameters --- a/test-data/arthropoda/clade_parameters Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -#ARTHROPODA Clade parameters for BUSCOS -Z 102785 -sp1 fly -sp2 nasonia -sp3 generic -flank 5000 |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm --- a/test-data/arthropoda/hmms/BUSCOaEOG7B0HST.hmm Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3319 +0,0 @@\n-HMMER3/f [3.1b1 | May 2013]\n-NAME BUSCOaEOG7B0HST\n-LENG 1099\n-ALPH amino\n-RF no\n-MM no\n-CONS yes\n-CS no\n-MAP yes\n-DATE Tue Apr 15 12:38:52 2014\n-NSEQ 23\n-EFFN 0.603638\n-CKSUM 3500044453\n-STATS LOCAL MSV -12.8285 0.69537\n-STATS LOCAL VITERBI -13.9416 0.69537\n-STATS LOCAL FORWARD -6.9634 0.69537\n-HMM A C D E F G H I K L M N P Q R S T V W Y \n- m->m m->i m->d i->m i->i d->m d->d\n- COMPO 2.48078 4.06146 2.86181 2.63028 3.29447 3.05836 3.78580 2.74928 2.73520 2.31160 3.52187 3.11102 3.40692 3.07770 2.99944 2.73817 2.93658 2.56860 4.67180 3.56430\n- 2.68613 4.42194 2.77509 2.73133 3.46348 2.40518 3.72504 3.29351 2.67743 2.69350 4.24642 2.90347 2.73745 3.18156 2.89802 2.37884 2.77522 2.98518 4.58487 3.61513\n- 0.08969 2.57172 4.66890 1.68962 0.20406 0.00000 *\n- 1 2.57261 4.35167 3.86119 3.40692 3.39776 3.63900 4.23782 2.41302 3.22676 2.05613 1.62924 3.68308 4.13489 3.59563 3.47552 3.02060 2.87665 2.31461 5.12383 3.92328 24 m - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 2 1.67850 4.50203 3.03694 2.37498 3.89784 3.30262 3.77719 3.19331 2.62660 2.92462 3.55380 3.06800 3.81401 2.99279 3.01679 2.53568 2.82599 2.89438 5.25006 3.96735 25 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 3 1.72593 4.51596 3.03450 2.62358 3.94870 3.02850 3.77178 3.31742 2.58759 2.83773 3.85577 3.06024 3.80166 2.49425 2.96418 2.62424 2.82773 2.99569 5.27761 3.99238 26 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 4 3.06989 5.20867 0.81737 2.38286 4.59580 3.26742 3.99737 4.20098 3.09568 3.79622 4.77615 2.94287 3.92548 3.23679 3.62179 3.02404 3.41012 3.83236 5.74996 4.45674 27 d - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 5 2.80194 4.77013 3.14922 2.71763 3.71311 3.52519 3.75923 3.19152 2.43092 2.26797 3.77243 3.16939 3.97062 1.69754 2.73211 2.88896 3.05024 3.01368 5.15367 3.80747 28 q - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 6 1.96528 5.02402 2.30355 2.05596 4.32542 3.05196 3.65086 3.77327 2.51296 3.33530 4.14888 2.71539 3.78621 2.65549 3.01420 2.66175 2.94409 3.40418 5.54285 4.15135 29 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.02912 3.94655 4.66890 0.61958 0.77255 0.48576 0.95510\n- 7 2.80616 5.09448 2.63904 2.23927 4.35587 3.37371 3.36290 3.83921 2.30093 3.36613 4.20407 2.73502 3.85607 1.67'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.03105 3.88362 4.60597 0.61958 0.77255 0.54401 0.86849\n- 1092 2.48411 4.80914 2.38269 2.16541 4.06714 3.19545 3.59049 3.47448 2.36289 3.08014 3.58530 2.86918 3.76448 2.73883 2.86648 2.59333 2.81189 2.86703 5.31779 3.97005 1199 e - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.03105 3.88362 4.60597 0.61958 0.77255 0.54401 0.86849\n- 1093 1.24199 4.14570 3.59318 3.27579 3.90565 3.06922 4.23995 2.85564 3.22241 2.82059 3.86698 3.41584 3.78036 3.55807 3.49165 2.52495 2.75938 2.36754 5.42950 4.19313 1200 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.06474 3.88362 3.16732 0.61958 0.77255 0.54401 0.86849\n- 1094 2.97106 4.49154 3.93866 3.46547 2.54041 3.89976 3.77718 2.63214 3.27427 1.57888 3.33399 3.70082 4.26271 3.58207 3.49841 3.23908 3.21105 2.56656 4.22346 1.92820 1201 l - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.03209 3.85097 4.57331 0.61958 0.77255 0.57161 0.83152\n- 1095 2.60101 4.65512 3.08558 2.56003 3.93846 3.38076 3.35844 3.37716 2.29364 2.98880 3.84025 3.01919 3.81697 2.81258 2.11081 2.23871 2.85240 2.88090 5.19817 3.90318 1202 r - - -\n- 2.68618 4.42210 2.77520 2.73124 3.46354 2.40513 3.72495 3.29354 2.67741 2.69355 4.24690 2.90347 2.73740 3.18147 2.89801 2.37883 2.77520 2.98519 4.58477 3.61504\n- 0.08263 2.67392 4.57331 0.47744 0.96856 0.57161 0.83152\n- 1096 2.18154 4.62997 2.75539 1.99629 4.09189 3.21947 3.71130 3.44588 2.55475 3.11415 3.95949 2.91659 3.75436 2.89454 2.98369 2.45299 2.43810 3.09910 5.37976 4.06153 1204 e - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.03209 3.85097 4.57331 0.61958 0.77255 0.52453 0.89608\n- 1097 2.46358 4.30538 3.37350 2.85594 3.45882 3.46342 3.46832 2.79047 2.73797 1.87351 3.43484 3.24873 3.57204 3.10968 3.06502 2.75631 2.66774 2.52856 4.91799 3.66813 1205 l - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.06381 3.88362 3.18837 0.61958 0.77255 0.54401 0.86849\n- 1098 1.76981 4.22446 3.25481 2.84716 3.91324 3.07102 3.91525 3.24756 2.83205 2.73784 3.84439 3.15656 3.31202 3.16923 3.18419 1.97191 2.69401 2.87700 5.28803 4.03807 1206 a - - -\n- 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n- 0.17726 3.85187 1.95758 0.61958 0.77255 0.57087 0.83249\n- 1099 2.12671 4.27681 2.94823 2.62386 4.02260 3.00213 3.81075 3.41128 2.69615 3.08313 3.92445 2.61229 3.24401 3.03239 3.07499 2.18871 2.34694 2.99753 5.34368 4.07427 1207 a - - -\n- 2.68560 4.42236 2.77531 2.73135 3.46365 2.40517 3.72506 3.29361 2.67747 2.69366 4.24701 2.90355 2.73729 3.18150 2.89812 2.37889 2.77501 2.98510 4.58488 3.61514\n- 0.29451 1.36610 * 1.25311 0.33633 0.00000 *\n-//\n' |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/arthropoda/lengths_cutoff --- a/test-data/arthropoda/lengths_cutoff Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG7B0HST 1099 16.763712248907 1099.28947368421 |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl --- a/test-data/arthropoda/prfl/BUSCOaEOG7B0HST.prfl Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1179 +0,0 @@\n-[name]\n-unknown\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-2\t136\n-\n-[block]\n-# block no. 0 follows, 38 sequences, length 19\n-# corresponding to MSA columns:\n-# 159-177\n-name=unknown_A\n-#\n-# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n-#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n-0\t0.00849\t0.00611\t0.00840\t0.00857\t0.00923\t0.00669\t0.00611\t0.00985\t0.00961\t0.01343\t0.01902\t0.11988\t0.02008\t0.26734\t0.45119\t0.00764\t0.01148\t0.00842\t0.00363\t0.00479\n-1\t0.04698\t0.19994\t0.01897\t0.01402\t0.05388\t0.40529\t0.01057\t0.01996\t0.01473\t0.02840\t0.01285\t0.12269\t0.01254\t0.00774\t0.00537\t0.00165\t0.00826\t0.00573\t0.00343\t0.00702\n-2\t0.10059\t0.05592\t0.04037\t0.12369\t0.03571\t0.33917\t0.01177\t0.05040\t0.04291\t0.12639\t0.01235\t0.01357\t0.00924\t0.00633\t0.00543\t0.00172\t0.00824\t0.00453\t0.00392\t0.00774\n-3\t0.00726\t0.00551\t0.00670\t0.00765\t0.00853\t0.00495\t0.00526\t0.00846\t0.01222\t0.01564\t0.04202\t0.55279\t0.26594\t0.01769\t0.00750\t0.00231\t0.00335\t0.01570\t0.00558\t0.00495\n-4\t0.01515\t0.01282\t0.01932\t0.01411\t0.01942\t0.01141\t0.20122\t0.08029\t0.06461\t0.07934\t0.01338\t0.01496\t0.01020\t0.00535\t0.00554\t0.00143\t0.00624\t0.00509\t0.00412\t0.41602\n-5\t0.01058\t0.00786\t0.01056\t0.13305\t0.01554\t0.00789\t0.00807\t0.01432\t0.07133\t0.05518\t0.29599\t0.18162\t0.03460\t0.01123\t0.00661\t0.00194\t0.00427\t0.02125\t0.02469\t0.08341\n-6\t0.05178\t0.16631\t0.50028\t0.01491\t0.02246\t0.01521\t0.03686\t0.01844\t0.01252\t0.01860\t0.01027\t0.01208\t0.00775\t0.00547\t0.00520\t0.00170\t0.00786\t0.00415\t0.00271\t0.08546\n-7\t0.01705\t0.01432\t0.01620\t0.01348\t0.01711\t0.07518\t0.07737\t0.22677\t0.26217\t0.05482\t0.04993\t0.11213\t0.01834\t0.00888\t0.00635\t0.00197\t0.00608\t0.00758\t0.00556\t0.00869\n-8\t0.01317\t0.01251\t0.02070\t0.15609\t0.52474\t0.01281\t0.01616\t0.01652\t0.01342\t0.01844\t0.01838\t0.02129\t0.11604\t0.00690\t0.00613\t0.00186\t0.00670\t0.00642\t0.00330\t0.00841\n-9\t0.01162\t0.00686\t0.00910\t0.00862\t0.01050\t0.00629\t0.00674\t0.01414\t0.01595\t0.14470\t0.42875\t0.11434\t0.07208\t0.01284\t0.00715\t0.00207\t0.00368\t0.11180\t0.00647\t0.00632\n-10\t0.01274\t0.01372\t0.12068\t0.01259\t0.01636\t0.01187\t0.04762\t0.04955\t0.31522\t0.02196\t0.05626\t0.13802\t0.02193\t0.00996\t0.00649\t0.00206\t0.00548\t0.07423\t0.00517\t0.05810\n-11\t0.00985\t0.00796\t0.01067\t0.01037\t0.01075\t0.00947\t0.00786\t0.01102\t0.01014\t0.01418\t0.01964\t0.14789\t0.02183\t0.26045\t0.10775\t0.00446\t0.21652\t0.11018\t0.00389\t0.00511\n-12\t0.00789\t0.00529\t0.00678\t0.00798\t0.00848\t0.00499\t0.00539\t0.00919\t0.01168\t0.01638\t0.03120\t0.67455\t0.03627\t0.01714\t0.00718\t0.00229\t0.00339\t0.01544\t0.12352\t0.00499\n-13\t0.00773\t0.00552\t0.00742\t0.00873\t0.00928\t0.00522\t0.00618\t0.00911\t0.01211\t0.01615\t0.06621\t0.64670\t0.03983\t0.01822\t0.00774\t0.00246\t0.00376\t0.11699\t0.00563\t0.00502\n-14\t0.23475\t0.01397\t0.01501\t0.05417\t0.12272\t0.06638\t0.01071\t0.11816\t0.17197\t0.11209\t0.01510\t0.01554\t0.01116\t0.00661\t0.00538\t0.00187\t0.00596\t0.00510\t0.00478\t0.00858\n-15\t0.01774\t0.01310\t0.01239\t0.01066\t0.01380\t0.13284\t0.00829\t0.12299\t0.12073\t0.17836\t0.04824\t0.03777\t0.12169\t0.04898\t0.00726\t0.00202\t0.00564\t0.00710\t0.08255\t0.00785\n-16\t0.00774\t0.00594\t0.00698\t0.00734\t0.00855\t0.00550\t0.00526\t0.00913\t0.01231\t0.01568\t0.07962\t0.21341\t0.34318\t0.13048\t0.08206\t0.00342\t0.00490\t0.04842\t0.00514\t0.00491\n-17\t0.01499\t0.01157\t0.01661\t0.08113\t0.01840\t0.01286\t0.11905\t0.12120\t0.08357\t0.07287\t0.05034\t0.01918\t0.01402\t0.00762\t0.00806\t0.00193\t0.13253\t0.00612\t0.20034\t0.00760\n-18\t0.02074\t0.06499\t0.01691\t0.01445\t0.01751\t0.60356\t0.01097\t0.07075\t0.01705\t0.01634\t0.01185\t0.08393\t0.01094\t0.00741\t0.00560\t0.00164\t0.00964\t0.00519\t0.00351\t0.00704\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-0\t1\n-\n-[block]\n-# block no. 1 follows, 38 sequences, length 22\n-# corresponding to MSA columns:\n-# 179-200\n-name=unknown_B\n-#\n-# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n-#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n-0\t0.08270\t0.19710\t0.02137\t0.01349\t0.01801\t0.06215\t0.13254\t0.04863\t0.19656\t0.08108\t0.01574\t0.01622\t0.02523\t0.00640\t0.00542\t0.00172\t0.00649\t0.00534\t0.00432\t0.05948\n-1\t0.01139\t0.00879\t0.01512\t0.01313\t0.01560\t0.00826\t0.17794\t0.01415\t0.01395\t0.08259\t0.12369\t0.26603\t0.03144\t0.01318\t0.00747\t0.00230\t0.00560\t0.17772\t0.0'..b'01399\t0.02763\t0.59409\t0.01622\t0.02410\t0.01459\t0.01966\t0.15312\t0.01578\t0.02277\t0.03493\t0.01405\t0.00968\t0.00621\t0.00582\t0.00189\t0.00827\t0.00483\t0.00333\t0.00904\n-17\t0.01558\t0.61804\t0.05875\t0.01338\t0.01885\t0.02182\t0.14636\t0.01829\t0.01261\t0.01530\t0.00917\t0.01100\t0.00798\t0.00515\t0.00454\t0.00145\t0.00722\t0.00399\t0.00266\t0.00784\n-18\t0.03107\t0.12435\t0.21748\t0.02929\t0.04145\t0.01280\t0.01239\t0.04101\t0.05280\t0.01971\t0.03883\t0.03793\t0.01160\t0.00601\t0.00512\t0.00147\t0.00610\t0.00477\t0.00351\t0.30232\n-19\t0.01371\t0.36393\t0.29683\t0.15693\t0.02425\t0.01821\t0.01591\t0.01790\t0.01236\t0.01619\t0.00970\t0.01198\t0.00774\t0.00552\t0.00495\t0.00165\t0.00764\t0.00407\t0.00258\t0.00796\n-20\t0.16658\t0.02744\t0.61619\t0.01540\t0.02332\t0.01388\t0.01926\t0.01879\t0.01224\t0.02055\t0.01034\t0.01215\t0.00741\t0.00569\t0.00534\t0.00190\t0.00809\t0.00422\t0.00276\t0.00844\n-21\t0.02417\t0.01022\t0.01334\t0.01041\t0.01471\t0.00913\t0.00853\t0.08055\t0.01774\t0.60573\t0.05239\t0.02435\t0.08388\t0.00832\t0.00618\t0.00187\t0.00496\t0.00679\t0.00713\t0.00960\n-22\t0.01677\t0.01205\t0.08140\t0.01031\t0.01522\t0.00893\t0.00905\t0.02045\t0.05274\t0.25615\t0.06649\t0.04544\t0.01557\t0.00678\t0.00547\t0.00148\t0.00495\t0.00560\t0.00513\t0.36003\n-23\t0.16683\t0.01180\t0.01496\t0.01290\t0.01423\t0.01516\t0.01064\t0.01467\t0.00977\t0.01725\t0.00928\t0.01378\t0.00863\t0.01340\t0.10939\t0.00321\t0.46410\t0.00488\t0.00300\t0.08213\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-7\t16\n-\n-[block]\n-# block no. 22 follows, 38 sequences, length 6\n-# corresponding to MSA columns:\n-# 1247-1252\n-name=unknown_W\n-#\n-# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n-#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n-0\t0.00733\t0.00524\t0.00698\t0.00838\t0.00873\t0.00489\t0.00558\t0.00838\t0.01152\t0.01536\t0.03316\t0.78466\t0.03979\t0.01885\t0.00768\t0.00244\t0.00349\t0.01710\t0.00558\t0.00489\n-1\t0.01041\t0.00709\t0.00808\t0.00738\t0.00993\t0.00599\t0.00575\t0.01235\t0.01441\t0.11123\t0.12398\t0.04824\t0.47386\t0.01304\t0.00680\t0.00193\t0.00356\t0.05072\t0.00575\t0.07949\n-2\t0.01430\t0.02608\t0.54722\t0.01765\t0.02555\t0.01352\t0.13402\t0.02039\t0.01351\t0.11246\t0.01266\t0.01425\t0.00878\t0.00583\t0.00598\t0.00192\t0.00861\t0.00507\t0.00324\t0.00894\n-3\t0.26692\t0.01203\t0.01543\t0.01222\t0.01656\t0.01225\t0.10707\t0.07068\t0.07963\t0.29248\t0.01726\t0.01826\t0.01233\t0.00696\t0.00558\t0.00193\t0.00575\t0.03264\t0.00543\t0.00857\n-4\t0.19703\t0.02395\t0.01536\t0.01387\t0.01690\t0.55243\t0.01062\t0.02202\t0.01505\t0.01736\t0.00901\t0.01077\t0.00749\t0.00635\t0.00600\t0.00169\t0.06019\t0.00383\t0.00320\t0.00685\n-5\t0.01450\t0.01539\t0.01823\t0.01575\t0.01620\t0.12585\t0.01294\t0.01585\t0.01034\t0.01451\t0.00810\t0.01283\t0.00788\t0.00991\t0.01768\t0.00248\t0.66716\t0.00506\t0.00270\t0.00664\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-0\t1\n-\n-[block]\n-# block no. 23 follows, 38 sequences, length 6\n-# corresponding to MSA columns:\n-# 1254-1259\n-name=unknown_X\n-#\n-# <colnr> <probs for GDERKNQSTAVLIFYWHMCP>\n-#\tG\tD\tE\tR\tK\tN\tQ\tS\tT\tA\tV\tL\tI\tF\tY\tW\tH\tM\tC\tP\n-0\t0.01343\t0.01028\t0.01283\t0.00977\t0.01415\t0.00866\t0.03490\t0.04640\t0.05049\t0.08028\t0.16725\t0.02064\t0.01996\t0.00666\t0.00539\t0.00132\t0.00449\t0.00567\t0.00472\t0.48271\n-1\t0.04265\t0.10015\t0.01305\t0.00922\t0.01226\t0.00970\t0.00754\t0.01866\t0.03805\t0.26240\t0.27072\t0.05409\t0.09335\t0.00992\t0.00664\t0.00187\t0.02797\t0.00820\t0.00606\t0.00751\n-2\t0.00774\t0.00584\t0.00715\t0.00741\t0.00866\t0.00525\t0.00533\t0.00963\t0.01433\t0.01908\t0.32409\t0.28450\t0.24864\t0.01522\t0.00729\t0.00211\t0.00311\t0.01338\t0.00600\t0.00525\n-3\t0.01099\t0.00669\t0.00941\t0.09845\t0.01363\t0.00652\t0.00742\t0.01259\t0.01250\t0.13528\t0.02900\t0.57076\t0.03203\t0.01550\t0.00722\t0.00230\t0.00428\t0.01393\t0.00554\t0.00596\n-4\t0.69880\t0.01184\t0.00961\t0.00861\t0.01228\t0.01373\t0.00700\t0.02000\t0.12855\t0.02669\t0.01099\t0.01183\t0.00844\t0.00600\t0.00411\t0.00189\t0.00467\t0.00383\t0.00411\t0.00700\n-5\t0.01499\t0.01161\t0.03484\t0.10038\t0.03814\t0.03077\t0.00958\t0.01979\t0.11229\t0.14220\t0.06861\t0.04057\t0.01539\t0.00673\t0.00552\t0.00153\t0.00526\t0.00563\t0.00467\t0.33149\n-\n-[dist]\n-# distance from previous block\n-# <min> <max>\n-12\t79\n-\n-# created by:\n-# /software/SequenceAnalysis/GenePrediction/augustus/3.0.1/scripts/msa2prfl.pl ./aligns/BUSCOaEOG7B0HST.fas\n' |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/arthropoda/scores_cutoff --- a/test-data/arthropoda/scores_cutoff Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -BUSCOaEOG7B0HST 996.48 |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/busco.loc --- a/test-data/busco.loc Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -arthropoda Arthropoda data ${__HERE__}/ |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/genome.fa --- a/test-data/genome.fa Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/genome.fa Mon Aug 17 06:50:18 2020 -0400 |
| b |
| b'@@ -1,14 +1,892 @@\n >sample\n-TGCATCGGTTATTTGCATTGGCTGGCATTTAATTTATGCACAAACACACACGCTGGAACACATTAGTCATACGCAACGTTGCACAAATATTTATTAGCTATTGCAAGTCAGTGCGGGGCAAATAGCACCGTGAAATGCAAACGAAAGCATTGAGTGTGCTGGCATCATCGATTTAGCAGCCATAAATACTGCTCAACACTAAATCAATCATACGCAATGTGGTGCTAATTGATTGAGCAAACATTGCCAAGATGCAATTGCCATGATCAAGG\n-GGCGAAGGTTTCTTTGGGCCAAACAGAAGAGTGGTTTCGCCACTTAACTAGAGGTTAATTATTAGATTGTATTAGCCAGCTAGCTGCGTACGAGCATATTGAGCTACTAATGATACCACAAGTTCGCAGTTATCGCCCCAGTGGAACCCTTGAGCTTAATCCCAGTGCCCCATTAAATACTTAAGCGCGGACCCTCCAGCGCTACTCCACTCGAGCGGTTCAACGAACTGGCCAGCACTCGAAACTAAAGCCCTACCATGATTCAATATCAA\n-GTTGGCAACTCGAAACCCACTTGGCATTAAGTATGACTGACCTGCAGGCGACTCAACCTCAACCTGAAGCTCAACCTGAAGCTCAACCGGCGCATTCAGCTCCAGCGTTTTGCATTTAGCATTCAGCCGTGTCCAATGCTAAGATCAATGCCACTCCACGCTGGCTGTGCCAACTTCCTGTTGCAGCAACCACTACTACCCTATATGGACACAATGTGCCACGCCACGAGTATAGTGTATCGTACCTACACGAGTATCTGGCCAGTCCGCAG\n-TCCTAGTTCTTCCCTGCTCCTTTTTATTTAAACACTTCCTCATTTCGCTTTGTGCCCTGGCATTTGGCAGCTATTCTGTGTCAATTCCCGGTGAGTGTCATTCGAACTGGTGAACCGGAGAATGGAGCAGTCGCCAGCCGAGGATTCAGAGCCAGAACCCCAAACCCAGAACCCAGAAGGCCAGGTGAATGGGATCGGGATTCACCCAGTCCTCGCTCGCCTGGCTGAGTGCCAAGTGTAGTGCAATAAACTTGCCGTCCTGAATGGCTGGC\n-AATCAAAGATCTGAATGCAAGATACGATGACATTTACTCGCACATTCAATTGCGCTTTTGATTTGAATATTTACATGCTTTCTGGTCGTAGTCCCAGTTCCGCAGACTCGAGTCCCTCGGGCTGCCATTCTTTCATGTCCTTTCGTTCTATTGACATAGTCAAATTGGCTTTGCTGCACAGCGAGAAAATGTACTTAACTTCCACACAATCCTGGCTATTTGCTGCTATGACTGTAAGCATAATTTATTTTAGGGTAAATGGGTGAGTGACC\n-AAAAGGCATGCCGTGCAGTTCATTTTATCAAAGCACCATGACTAACTGGTACAACCATTTTTTCTGCGTGCCTTTCGGGTCAACCGAATCAGGCCCTAATTGATTTTCAAATGTTTCCACAGCGTCTTAAAGTCCAGTCCTTATTTAAACAACTTACTAAGTATTGCAGAGCCTTGGCATACTTAGCTGCAGTTATGCATTTCAAGCATAAACAACTAATTTGACTAATTGATAAGCCATGCAAAGGCAAAGGCATCTCGAGATGTCTTGAG\n-TCGACTTCACTGCACTTCTGGCCGGCTTGTCTCGGCCTGGTTGGTTGCGTTTCTGTATCTTTGGCTCCGGCTGTTTGCTTTGTCCATCAACATCTTTTGAGCGGAGGCACTCAGGCGCAAACTGTTGCACTTCAGACCAGTCTGGAGAGCAGTGTTCACTAGGATACGAGTATATACATAGGCTCATGTGGAGCCGGGATCAAGCCACCCCAAACCCCAAACCCCATTAATTGCAATCAATTTCGCTGTCAACACACACTCCAAATAACTGC\n-GGGATATTTATTTATGGGCTGCGCTTCCCTTCAGCAACCTTTTGCAACTGAATAATTGCCTTATGACACATTATCATTATTATTAAGGCTGCCACGGGTCGGCAAAGTAATCATTACCTCCTGCCCATATCATCCTGCCCCTGGGCCATGAACCTGGGAATTAGGGAGTCAGCATTGCAGTGCCCACAGCTCCTCTATGCTCATAAATATATTTCCAGCTGGCAACATTATATAATTATTTTGCCATGGATTGCATTGAACTTAGTCCGAGT\n-GCGTCGATGTTGCTCGTTTGCTGTTTGCTGTTTGCTATTTCTGTTTGCACTTCTTGCCGCAGGCGCGCAACTCTTCATGTGGCTTCTTCTCGTTTTTAGGCCAGAATCCAGAAGGCAGCGTTCAGAACCCAGAATCCAGAATCCATGTGATGCCTTTGCGTGAATTTCATTTTAAAGTGCAAATATTTGCGGCCTGGCCCGGCCAGTTGCTTAAATGGAAAACTGGGCGAGAAAAAAGAATGCACTGGTAGCTCACAAACAGCCCACACAGA\n-AACCAGTAATGAAATTGTGCGGCACTCGTCATTGCGGCACTGGCCTTACATATAAATTATATAAAATATATACACATTTGTTTGGCATTGACCGGCCTACAAAGGAACTGCAGCCAGGGATGCAGCATGGGTATGATTTCCCTATAGTCGTGGCAAATACCTTTAACACGAGTAAGTACAAGTAATGCCCAACTGAGGGCCTTCAAGTAATATTAAGAGAAGATATTTTTAAACATCTATCTTTTTTAAGGACACACATTCTAACTTTATTT\n-ACGAGAGACACTGGCACCCTCATACAAAATTCTAGAAAGCTAGTCAGTAAACTAGAACTGCAGTTCTCCCCTGCTTATGACAATAACAGCAATTTGTATTTAAATTTAGGAATGACCAGGGCTCTTCCGCTCCACCCTGGCCAGTATAATTTGTGCATCTCTAGCCAATACAAACTTATTATATACTTGCAAAAGTTGTGCACTGTAAATATTTGCGGCGACCACCCGCACTTTCGCCATGACTACAAAATGGGTGGCATGAAATGGGGGCT\n-TTTGGGGGGCAACCGCAGAGAATGCTTGACTTTGGCCGGTAAAAAACTACGCAGACCACCCACCACCCAACCCGGTTTTTCTCTCTTGGCCACGTTTATTGATGGCGGCGGGAAGTGCTTTAATGGAAATTTAAGTATCATCGTTTAAAATGAAGCAGAAAAGCGCAAGCGAACGAAAGACCCTGGAAAATTGCGAGTTGCGACTGGTATTGCGACCCTTGAGCTTTGGTCATTGCGTTGGCAACGCAAATTATTATTTTTATTATTATTGC\n-AGGTTTTCGGTGCACATTTATTTCATGCAACTTTACAGCGCTGCACATAGAAATTATGTACAGGCCGCGTGGGCCATAATGCAGATTGCCAACCCGAGAAGGGTAACTCGGAGTGAAATGGCGGGAATTAGGCAAGCAAACAGGCAACTAAAATATGCAACGCAGGCAGTGGGGAAATTTGATGGGCGCCAGAAAAGGCCGTGAAAAGGCCGTAAAACTGGGCCAAGTAATGAGCTACGGCGGCCACACATTAAATATGCAACAATTAAAAG\n+GTGGCCGGCTGATTTCACGTCCTAACTTTGGGCTTAACTGGTTCGCCAGTTGACTTTCTTCGCCATCATG\n+TGATGCATTAATTAAACAATAATTACTAATTGACAGTAATTAATAATTGTGGCAAAAAGCGCGACACGTT\n+TTTTCGGCAAACTCCTCGGAAGACCGATTGTTTAAAGACGTAGGGAAAAGTAGTTCCCAAGCATTTTAAA\n+AAGATACCTATGACATGTGACACCTTTAAAGTGCAATACAAGTTTTCATCTCTTTATATCCTTTTACTCC\n+CTAATTTGAATATAAAAGGAATCGCATTGAGAGTATAAAGGCTTTAGTTCTTATCGATAGATAGTTAGTG\n+ATGAAATAAAATTATAACCGTGGTTTTAGTTTGAAATGTTGTAAAGAC'..b'AAAAGTTCAAATTTAGGCGGTAACAAAAATAGCACTGT\n+TTCTCGTAGTTTGCTAAAACTAACCAAAAAAAAATAAAAAAATAATTCAACAAATGAATTATATCTTAAG\n+AACTATGTTTAAAGAATCTTAATATTTGGTTGCGTGACCTTTGTTGGCAATGACAGCCGCGCATCGTCCT\n+GGCATGGAGTCCACCAAGTCCTGGCATCGTTATTGAGTAGTTTTGCTCCATGGATCCTTGACCAGACCCC\n+AAAGATCATCGTTATTATTGGGTTTGGCTTCAGAGACCTTTTTTTCACGTCCGCCCAAAGGTTTTCGATT\n+GGATTCAAGTCGGGTGACTGAGCAGGCCAGTTCATTCCTCGGATCGATTTCTGCTCTAACCACTTTCGAG\n+CGTTCTTCCTCGTGTGTTTTGGGTCGTTATCCTGTTGAAATATTCAAACCAACGGCATTTCATCCTCGGC\n+ATATGACAGCATCACATTTTCCAGGATATCTGTGTAAATGTCCTGATCCATGATGCCTTGAATCTAATGG\n+ATCGGACCTACTCCATAGTACGAAAAGCACGCCCGTACCATTGTGTTTGATCCCCCGTACTTTACCGCCT\n+TAAAGGTGAAGCGAGGATTATATTCAGTTCGTGGAGGACGCCGAACATAAGACCAAGACAACACAAACAA\n+CACAATTTTGGTCTCATCTGACCACAAAATGTTGCGCCACTTCTCCACAGGCCAGTCCTTGGGAATCTTG\n+GCATATTCTATTCGCTTTGCCACATGCTTAACAGTCAAAAGCGGGACTTTTCTTGGGCTGCACGCATTAA\n+GGTTGTTTTGTTTTTATTTTTTTTTTTTTTTTGTTTTATTATTCATGCAATCTGACTTTAAAAAATATAA\n+ACATTTAATAATTTTTTTTTGAAAATGAACTTTCCACCTGCAATAGTGCTATTATTTTAAACGCAGCTGT\n+ATAACTAATTGTGTCGTTTATTATAGATTTTTTAAGAAGTAATATAATTTGGTTGCATGTGATTATTGGA\n+GTATTCCTTCGTTACGATGTGAAAACTACATATTTATGAAATTGCCAACTGCTAATTGAACAAAAACCCG\n+ACAAAAGTGCTGCTAATGGACAAAACACATATAACACAAATGGCACAGACAACGGACAACAAACCGCCCA\n+TCGACAAGGGTCGCAAATTGGGAGGAAATACAAACAGATGGAAATCTGTGTATAAAACCCAAGCAACCCG\n+AAGTGGAGAAACTGGAAATGTGAAAAGCGCGGCATGCGGCCCAAGTCAGCGGGGGCGACCAATAGGTCAA\n+GTACGAACTGCATTGGCTCGCTTTAGTTTTAGCGGCTCCGGAAGTGAAACAGTTTGATGGAGCCCTGACG\n+TGGGCAGAACTACGCGTGCCAAAAGGTGCACAGAGGCCTTAGCGGAATTCGGAAGACAGCTGGTTTTCAT\n+TCACAATTCACAATTTACAATACGCAATTATGCAATAAAAGGTGGCGAACTTAAATGCAACCTGGTATTC\n+TAAACATAATGCTGGGAAAACAATGACCATGGGCCAAATGGTGGTTAAAATTCACCACCTCTCCTTTTTT\n+GGTAACAGGAAAGTGATGGCATTATTTATTGACAAAATTCAACGAAATCCATTATAAATATACATGTAAG\n+TCACAAGCCCCCTATATGGCCTTTGGAAAATGCTATACTTACTTTGTTTGGCAGTCAAGTCGGTTGCTCA\n+CAGTACGAAATGAGCTGAGTTGGCAGCACTGATTGTAAGTCGCTTTCCCGCTCGCACGCCGCTCGGCTGT\n+CTCCGTCCTTGTTTGGCATCCACCACTGCGCTCCTCCGCCCGCCTGCCTGTAGTCATTTCTCATCGCCAC\n+CGGGTTGTTTCCTTGTAATTTGTCACCGCTGGAGCCCATTTCTGCGGCGTAATTTGTTTGCAACTCATTT\n+CGGGATTCATTTCCATGGCTGGGTTGTCTCTTTGTTTGCTTGCCTTTGTTTTGGTCAGCTGCCTTGGGCT\n+CGGTGCATTTAATTAAAATTATTATTGCTTGTAATTGGGGAGCGAAGGTGGGTTATTCGTAGGGTCAAAT\n+AAGCAGACCGACTTGCATTACAACGTTTTACGGAATGAAGTGTCAATGTAATGCAACCGAGAAATTGAAA\n+GCTATATTTTGGAGTAAGTTTGAGGCTATTTTTATCAACCTTTAAGGAATTGGTGATATGGCGATATTTG\n+ATAACAGTCCACAAAGTATTTTATAAGCCATAAAGGGCCCCCCTAAGTTTAAGCCATTAAGGGCAGGGGG\n+TTCCTTCGATTAATCGATTTGGTTTCAACTCAAGAGAAGCCTGACCAGATAAAATTTATTGTCAGGGCAG\n+AAAACCGATCACACTCAGTTTCTACGATCGCCCTAATATTTGGAAATCGACCAACGCTTCTTCTTTGTGG\n+AAAGTACTTGTTGAAGTGCAACTCGGCCTGTGGCCATCTTGCACATAAGGAAACATTTTGAAATACTTTT\n+AATTTCATTCACCTTCCCTCTTTCATTTTAGGCCCCCCACAACCAAAACTCTTTCAAAATATCTTTCCAC\n+TCACTTCATTACCAACTGAGGCATATCAATTTGGCCTATCCATACAAAGTAAGCCACTTCAGAAAACTAA\n+TTTTTGAGCATTAGAAAGGTCTGGGCCTACACATATGGATGTATATATGTACCTATATGAATGTAGTTCC\n+ACGGCGATTGTGATCCAGCATGACTTTGCTTTCAAAACATATTTGCAACGGCGAAAAGCCGACAACAATA\n+GAGTAACACTCCCGTCATAAAGGAAAAGTATAAAAAATTCTCAAGTACACGCACTTTTGAACGCAATTAC\n+GTTGAACTTGGGCTCATGGCATGGGGTGGTGTGCAGGGTGCAGGGGGTATGGGCATAGGATTGTTGAAAC\n+GAACTTTACAATAATATTCGTGTGTAAGTCTTAACGATGGCAGCGAAGAAAATTTTTTTATTTGCCTTGG\n+GGCGAAACTTGAATCGGATTTGCACTCTATTGACTTCTGCGCCGCTCCCCCTATTACTTATTCTGCACCG\n+CGTAGTTGCACAATCCAGAATGACCCAGGTAGAAAAAGAAGATCCATTCAATTTCTCGCATAGGACCGCA\n+TACCCTGTAAAAACTGTTTTACTATATAAGTATTGTAAGTGTAATATGAATAGTACGAGTATAGATCCAA\n+TGAAATGGATATTTGGTGGAGTAAACCGAAAGTTATCGAAGATTCCATTATGAGTGCTCTAATAGCTCCA\n+CTATGATTTAAAATTACCAAAACCTATCAACCGAATGAAACAACAACAACGACGACAACTGGAATGCATC\n+ACCATCAACACATCGTCGCAGTTCACCACACTATCGCCATCTCGCTTTTCCATCGCCATTGGGGGTTCGG\n+CATTGATACTGCGCCTATGCGTGCATCCCGCTTGCTCTCCCGTCCGCATTCGCACCCTAGAGCCCTCGCT\n+GTCTCACTCCCTCTCCCTTTCCAACAACACATTCATCCTGAGACCCTTTGCGAGCGGATTTGGCTTTATT\n+AGTTTGTCTAATTGCTTTTTGCAACAATTATTACGGCATTTTCGTTTTTGTCGCCGGTGTGTTGTTAGTT\n+CTCGCAGCAGAAAAGTATCACAGATGTGTGAGCCCCGCGCTGACACCCCGCGGATTTGCTAGGCTTTGAT\n+TTGACTCCTGGCATGTTTTGTTGTAATTGTACATAGCGCTCGTACTCGATTTTCAATTTTGGGTGTGCTT\n+TGGTTACCATGTTCTGTTAGGCATAGAGCGCGCGATTCATCTCTCTGGGCTACTACTTTTCTAATATTTT\n+TTAATAAATTCTGTTAAAGAAGGCGTGAAACATTTCACTGTTTCAGCATTTCTGTTTCTAGGTACCGCCC\n' |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/genome_results/full_table --- a/test-data/genome_results/full_table Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/genome_results/full_table Mon Aug 17 06:50:18 2020 -0400 |
| b |
| b'@@ -1,6 +1,1016 @@\n-# BUSCO version is: 3.0.2 \n-# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A)\n-# 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\n-#\n-# Busco id\tStatus\tContig\tStart\tEnd\tScore\tLength\n-BUSCOaEOG7B0HST\tMissing\n+# BUSCO version is: 4.1.2 \n+# The lineage dataset is: arthropoda_odb10 (Creation date: 2019-11-20, number of species: 90, number of BUSCOs: 1013)\n+# Busco id\tStatus\tSequence\tGene Start\tGene End\tScore\tLength\tOrthoDB url\tDescription\n+774at6656\tMissing\n+980at6656\tMissing\n+997at6656\tMissing\n+1166at6656\tMissing\n+1885at6656\tMissing\n+1990at6656\tMissing\n+2148at6656\tMissing\n+2456at6656\tMissing\n+2473at6656\tMissing\n+3310at6656\tMissing\n+3585at6656\tMissing\n+3644at6656\tMissing\n+4136at6656\tMissing\n+4227at6656\tMissing\n+4864at6656\tMissing\n+5277at6656\tMissing\n+5616at6656\tMissing\n+6453at6656\tMissing\n+6563at6656\tMissing\n+6715at6656\tMissing\n+6820at6656\tMissing\n+7210at6656\tMissing\n+8145at6656\tMissing\n+8495at6656\tMissing\n+8847at6656\tMissing\n+8913at6656\tMissing\n+9647at6656\tMissing\n+9648at6656\tMissing\n+10240at6656\tMissing\n+10573at6656\tMissing\n+11384at6656\tMissing\n+12029at6656\tMissing\n+12174at6656\tMissing\n+12383at6656\tMissing\n+12771at6656\tMissing\n+12846at6656\tMissing\n+13019at6656\tMissing\n+13051at6656\tMissing\n+13736at6656\tMissing\n+13833at6656\tMissing\n+13858at6656\tMissing\n+13890at6656\tMissing\n+13934at6656\tMissing\n+14090at6656\tMissing\n+14257at6656\tMissing\n+14447at6656\tMissing\n+14995at6656\tMissing\n+15200at6656\tMissing\n+15697at6656\tMissing\n+15905at6656\tMissing\n+16061at6656\tMissing\n+16084at6656\tMissing\n+16220at6656\tMissing\n+16630at6656\tMissing\n+16648at6656\tMissing\n+17096at6656\tMissing\n+17122at6656\tMissing\n+17128at6656\tMissing\n+17748at6656\tMissing\n+18036at6656\tMissing\n+18055at6656\tMissing\n+18073at6656\tMissing\n+18630at6656\tMissing\n+18929at6656\tMissing\n+19044at6656\tMissing\n+19058at6656\tMissing\n+19104at6656\tMissing\n+19129at6656\tMissing\n+19208at6656\tMissing\n+19289at6656\tMissing\n+19590at6656\tMissing\n+19760at6656\tMissing\n+20093at6656\tMissing\n+20162at6656\tMissing\n+20267at6656\tMissing\n+20935at6656\tMissing\n+20936at6656\tMissing\n+21019at6656\tMissing\n+21191at6656\tMissing\n+21361at6656\tMissing\n+21367at6656\tMissing\n+21385at6656\tMissing\n+22098at6656\tMissing\n+22148at6656\tMissing\n+22358at6656\tMissing\n+22364at6656\tMissing\n+22468at6656\tMissing\n+22611at6656\tMissing\n+22887at6656\tMissing\n+23309at6656\tMissing\n+23388at6656\tMissing\n+23429at6656\tMissing\n+23917at6656\tMissing\n+24255at6656\tMissing\n+24427at6656\tMissing\n+24459at6656\tMissing\n+24556at6656\tMissing\n+24573at6656\tMissing\n+25554at6656\tMissing\n+25680at6656\tMissing\n+26078at6656\tMissing\n+26653at6656\tMissing\n+26734at6656\tMissing\n+27198at6656\tMissing\n+27515at6656\tMissing\n+27617at6656\tMissing\n+27655at6656\tMissing\n+28325at6656\tMissing\n+28380at6656\tMissing\n+28519at6656\tMissing\n+28685at6656\tMissing\n+28872at6656\tMissing\n+29213at6656\tMissing\n+29237at6656\tMissing\n+29365at6656\tMissing\n+29730at6656\tMissing\n+29744at6656\tMissing\n+30156at6656\tMissing\n+30184at6656\tMissing\n+30267at6656\tMissing\n+30463at6656\tMissing\n+30512at6656\tMissing\n+30526at6656\tMissing\n+30642at6656\tMissing\n+30822at6656\tMissing\n+30918at6656\tMissing\n+30962at6656\tMissing\n+31014at6656\tMissing\n+31119at6656\tMissing\n+31196at6656\tMissing\n+31333at6656\tMissing\n+31480at6656\tMissing\n+31615at6656\tMissing\n+31634at6656\tMissing\n+31820at6656\tMissing\n+31886at6656\tMissing\n+31919at6656\tMissing\n+32694at6656\tMissing\n+32733at6656\tMissing\n+32851at6656\tMissing\n+33187at6656\tMissing\n+33566at6656\tMissing\n+33794at6656\tMissing\n+34586at6656\tMissing\n+34917at6656\tMissing\n+35035at6656\tMissing\n+35548at6656\tMissing\n+35680at6656\tMissing\n+35708at6656\tMissing\n+35995at6656\tMissing\n+36374at6656\tMissing\n+36387at6656\tMissing\n+36403at6656\tMissing\n+36463at6656\tMissing\n+37030at6656\tMissing\n+37297at6656\tMissing\n+37387at6656\tMissing\n+37678at6656'..b'90at6656\tMissing\n+135702at6656\tMissing\n+135764at6656\tMissing\n+135828at6656\tMissing\n+135834at6656\tMissing\n+135859at6656\tMissing\n+135975at6656\tMissing\n+135994at6656\tMissing\n+136055at6656\tMissing\n+136095at6656\tMissing\n+136119at6656\tMissing\n+136224at6656\tMissing\n+136365at6656\tMissing\n+136559at6656\tMissing\n+136888at6656\tMissing\n+137050at6656\tMissing\n+137197at6656\tMissing\n+137202at6656\tMissing\n+137334at6656\tMissing\n+137338at6656\tMissing\n+137422at6656\tMissing\n+137609at6656\tMissing\n+137688at6656\tMissing\n+137709at6656\tMissing\n+137711at6656\tMissing\n+138243at6656\tMissing\n+138271at6656\tMissing\n+138379at6656\tMissing\n+138401at6656\tMissing\n+138502at6656\tMissing\n+138553at6656\tMissing\n+138659at6656\tMissing\n+138684at6656\tMissing\n+138937at6656\tMissing\n+139217at6656\tMissing\n+139553at6656\tMissing\n+139638at6656\tMissing\n+139744at6656\tMissing\n+139834at6656\tMissing\n+140076at6656\tMissing\n+140197at6656\tMissing\n+140198at6656\tMissing\n+140403at6656\tMissing\n+140461at6656\tMissing\n+140693at6656\tMissing\n+140874at6656\tMissing\n+140903at6656\tMissing\n+141031at6656\tMissing\n+141163at6656\tMissing\n+141166at6656\tMissing\n+141175at6656\tMissing\n+141298at6656\tMissing\n+141804at6656\tMissing\n+141859at6656\tMissing\n+141916at6656\tMissing\n+142388at6656\tMissing\n+142415at6656\tMissing\n+142522at6656\tMissing\n+142613at6656\tMissing\n+142661at6656\tMissing\n+142833at6656\tMissing\n+143154at6656\tMissing\n+143279at6656\tMissing\n+143459at6656\tMissing\n+143489at6656\tMissing\n+143562at6656\tMissing\n+143626at6656\tMissing\n+143709at6656\tMissing\n+143812at6656\tMissing\n+143930at6656\tMissing\n+144337at6656\tMissing\n+144652at6656\tMissing\n+144836at6656\tMissing\n+144851at6656\tMissing\n+144853at6656\tMissing\n+145033at6656\tMissing\n+145102at6656\tMissing\n+145443at6656\tMissing\n+145610at6656\tMissing\n+145811at6656\tMissing\n+145996at6656\tMissing\n+146007at6656\tMissing\n+146036at6656\tMissing\n+146087at6656\tMissing\n+146102at6656\tMissing\n+146103at6656\tMissing\n+146383at6656\tMissing\n+146600at6656\tMissing\n+146920at6656\tMissing\n+147002at6656\tMissing\n+147025at6656\tMissing\n+147322at6656\tMissing\n+147657at6656\tMissing\n+147723at6656\tMissing\n+147852at6656\tMissing\n+147891at6656\tMissing\n+147980at6656\tMissing\n+148134at6656\tMissing\n+148619at6656\tMissing\n+148713at6656\tMissing\n+148851at6656\tMissing\n+148890at6656\tMissing\n+149101at6656\tMissing\n+149126at6656\tMissing\n+149251at6656\tMissing\n+149405at6656\tMissing\n+149680at6656\tMissing\n+149753at6656\tMissing\n+149796at6656\tMissing\n+149819at6656\tMissing\n+149973at6656\tMissing\n+149977at6656\tMissing\n+150005at6656\tMissing\n+150049at6656\tMissing\n+150137at6656\tMissing\n+150182at6656\tMissing\n+150251at6656\tMissing\n+150327at6656\tMissing\n+150479at6656\tMissing\n+150583at6656\tMissing\n+150585at6656\tMissing\n+150667at6656\tMissing\n+150765at6656\tMissing\n+151102at6656\tMissing\n+151111at6656\tMissing\n+151114at6656\tMissing\n+151393at6656\tMissing\n+151436at6656\tMissing\n+151642at6656\tMissing\n+151658at6656\tMissing\n+152032at6656\tMissing\n+152109at6656\tMissing\n+152402at6656\tMissing\n+152534at6656\tMissing\n+152871at6656\tMissing\n+153155at6656\tMissing\n+153232at6656\tMissing\n+153312at6656\tMissing\n+153534at6656\tMissing\n+153693at6656\tMissing\n+153873at6656\tMissing\n+154133at6656\tMissing\n+154415at6656\tMissing\n+154507at6656\tMissing\n+155285at6656\tMissing\n+156057at6656\tMissing\n+156081at6656\tMissing\n+156111at6656\tMissing\n+156305at6656\tMissing\n+156395at6656\tMissing\n+156728at6656\tMissing\n+156824at6656\tMissing\n+156882at6656\tMissing\n+156975at6656\tMissing\n+157486at6656\tMissing\n+157579at6656\tMissing\n+157851at6656\tMissing\n+157879at6656\tMissing\n+158194at6656\tMissing\n+158760at6656\tMissing\n+159231at6656\tMissing\n+159420at6656\tMissing\n+159542at6656\tMissing\n+160675at6656\tMissing\n+160705at6656\tMissing\n+161435at6656\tMissing\n+162059at6656\tMissing\n+162147at6656\tMissing\n+162594at6656\tMissing\n+162628at6656\tMissing\n+162841at6656\tMissing\n+163670at6656\tMissing\n+163896at6656\tMissing\n+164354at6656\tMissing\n+164512at6656\tMissing\n+165142at6656\tMissing\n+165207at6656\tMissing\n+165493at6656\tMissing\n+166476at6656\tMissing\n+166479at6656\tMissing\n+166485at6656\tMissing\n+169220at6656\tMissing\n' |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/genome_results/missing_buscos_list --- a/test-data/genome_results/missing_buscos_list Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/genome_results/missing_buscos_list Mon Aug 17 06:50:18 2020 -0400 |
| b |
| b'@@ -1,5 +1,1015 @@\n-# BUSCO version is: 3.0.2 \n-# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A)\n-# 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\n-#\n-BUSCOaEOG7B0HST\n+# BUSCO version is: 4.1.2 \n+# The lineage dataset is: arthropoda_odb10 (Creation date: 2019-11-20, number of species: 90, number of BUSCOs: 1013)\n+# Busco 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|
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/genome_results/short_summary --- a/test-data/genome_results/short_summary Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/genome_results/short_summary Mon Aug 17 06:50:18 2020 -0400 |
| [ |
| @@ -1,15 +1,14 @@ -# 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 +# BUSCO version is: 4.1.2 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2019-11-20, number of species: 90, number of BUSCOs: 1013) +# Summarized benchmarking in BUSCO notation for file /tmp/tmpsafr8yho/files/4/1/7/dataset_417da650-712e-4081-86f4-3edaae2d6232.dat # BUSCO was run in mode: genome - C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:1 + ***** Results: ***** - 0 Complete BUSCOs (C) - 0 Complete and single-copy BUSCOs (S) - 0 Complete and duplicated BUSCOs (D) - 0 Fragmented BUSCOs (F) - 1 Missing BUSCOs (M) - 1 Total BUSCO groups searched + C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 + 1 Complete BUSCOs (C) + 1 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 1012 Missing BUSCOs (M) + 1013 Total BUSCO groups searched |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/proteome_results/full_table --- a/test-data/proteome_results/full_table Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/proteome_results/full_table Mon Aug 17 06:50:18 2020 -0400 |
| b |
| b'@@ -1,6 +1,1016 @@\n-# BUSCO version is: 3.0.2 \n-# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A)\n-# 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\n-#\n-# Busco id\tStatus\tSequence\tScore\tLength\n-BUSCOaEOG7B0HST\tFragmented\tBUSCOaEOG7B0HST\t1877.5\t899\n+# BUSCO version is: 4.1.2 \n+# The lineage dataset is: arthropoda_odb10 (Creation date: 2019-11-20, number of species: 90, number of BUSCOs: 1013)\n+# Busco id\tStatus\tSequence\tScore\tLength\tOrthoDB url\tDescription\n+774at6656\tMissing\n+980at6656\tMissing\n+997at6656\tMissing\n+1166at6656\tMissing\n+1885at6656\tMissing\n+1990at6656\tMissing\n+2148at6656\tMissing\n+2456at6656\tMissing\n+2473at6656\tMissing\n+3310at6656\tMissing\n+3585at6656\tMissing\n+3644at6656\tMissing\n+4136at6656\tMissing\n+4227at6656\tMissing\n+4864at6656\tMissing\n+5277at6656\tMissing\n+5616at6656\tMissing\n+6453at6656\tMissing\n+6563at6656\tMissing\n+6715at6656\tMissing\n+6820at6656\tMissing\n+7210at6656\tMissing\n+8145at6656\tMissing\n+8495at6656\tMissing\n+8847at6656\tMissing\n+8913at6656\tMissing\n+9647at6656\tMissing\n+9648at6656\tMissing\n+10240at6656\tMissing\n+10573at6656\tMissing\n+11384at6656\tMissing\n+12029at6656\tMissing\n+12174at6656\tMissing\n+12383at6656\tMissing\n+12771at6656\tMissing\n+12846at6656\tMissing\n+13019at6656\tMissing\n+13051at6656\tMissing\n+13736at6656\tMissing\n+13833at6656\tMissing\n+13858at6656\tMissing\n+13890at6656\tMissing\n+13934at6656\tMissing\n+14090at6656\tMissing\n+14257at6656\tMissing\n+14447at6656\tMissing\n+14995at6656\tMissing\n+15200at6656\tMissing\n+15697at6656\tMissing\n+15905at6656\tMissing\n+16061at6656\tMissing\n+16084at6656\tMissing\n+16220at6656\tMissing\n+16630at6656\tMissing\n+16648at6656\tMissing\n+17096at6656\tMissing\n+17122at6656\tMissing\n+17128at6656\tMissing\n+17748at6656\tMissing\n+18036at6656\tMissing\n+18055at6656\tMissing\n+18073at6656\tMissing\n+18630at6656\tMissing\n+18929at6656\tMissing\n+19044at6656\tMissing\n+19058at6656\tMissing\n+19104at6656\tMissing\n+19129at6656\tMissing\n+19208at6656\tMissing\n+19289at6656\tMissing\n+19590at6656\tMissing\n+19760at6656\tMissing\n+20093at6656\tMissing\n+20162at6656\tMissing\n+20267at6656\tMissing\n+20935at6656\tMissing\n+20936at6656\tMissing\n+21019at6656\tMissing\n+21191at6656\tMissing\n+21361at6656\tMissing\n+21367at6656\tMissing\n+21385at6656\tMissing\n+22098at6656\tMissing\n+22148at6656\tMissing\n+22358at6656\tMissing\n+22364at6656\tComplete\tBUSCOaEOG7B0HST\t1355.6\t788\thttps://www.orthodb.org/v10?query=22364at6656\timportin-5\n+22468at6656\tMissing\n+22611at6656\tMissing\n+22887at6656\tMissing\n+23309at6656\tMissing\n+23388at6656\tMissing\n+23429at6656\tMissing\n+23917at6656\tMissing\n+24255at6656\tMissing\n+24427at6656\tMissing\n+24459at6656\tMissing\n+24556at6656\tMissing\n+24573at6656\tMissing\n+25554at6656\tMissing\n+25680at6656\tMissing\n+26078at6656\tMissing\n+26653at6656\tMissing\n+26734at6656\tMissing\n+27198at6656\tMissing\n+27515at6656\tMissing\n+27617at6656\tMissing\n+27655at6656\tMissing\n+28325at6656\tMissing\n+28380at6656\tMissing\n+28519at6656\tMissing\n+28685at6656\tMissing\n+28872at6656\tMissing\n+29213at6656\tMissing\n+29237at6656\tMissing\n+29365at6656\tMissing\n+29730at6656\tMissing\n+29744at6656\tMissing\n+30156at6656\tMissing\n+30184at6656\tMissing\n+30267at6656\tMissing\n+30463at6656\tMissing\n+30512at6656\tMissing\n+30526at6656\tMissing\n+30642at6656\tMissing\n+30822at6656\tMissing\n+30918at6656\tMissing\n+30962at6656\tMissing\n+31014at6656\tMissing\n+31119at6656\tMissing\n+31196at6656\tMissing\n+31333at6656\tMissing\n+31480at6656\tMissing\n+31615at6656\tMissing\n+31634at6656\tMissing\n+31820at6656\tMissing\n+31886at6656\tMissing\n+31919at6656\tMissing\n+32694at6656\tMissing\n+32733at6656\tMissing\n+32851at6656\tMissing\n+33187at6656\tMissing\n+33566at6656\tMissing\n+33794at6656\tMissing\n+34586at6656\tMissing\n+34917at6656\tMissing\n+35035at6656\tMissing\n+35548at6656\tMissing\n+35680at6656\tMissing\n+35708at6656\tMissing\n+35995at6656\tMissing\n+36374at6656\tMissing\n+36387at6656\tMissing\n+36403at6656\tMissing\n+36463a'..b'90at6656\tMissing\n+135702at6656\tMissing\n+135764at6656\tMissing\n+135828at6656\tMissing\n+135834at6656\tMissing\n+135859at6656\tMissing\n+135975at6656\tMissing\n+135994at6656\tMissing\n+136055at6656\tMissing\n+136095at6656\tMissing\n+136119at6656\tMissing\n+136224at6656\tMissing\n+136365at6656\tMissing\n+136559at6656\tMissing\n+136888at6656\tMissing\n+137050at6656\tMissing\n+137197at6656\tMissing\n+137202at6656\tMissing\n+137334at6656\tMissing\n+137338at6656\tMissing\n+137422at6656\tMissing\n+137609at6656\tMissing\n+137688at6656\tMissing\n+137709at6656\tMissing\n+137711at6656\tMissing\n+138243at6656\tMissing\n+138271at6656\tMissing\n+138379at6656\tMissing\n+138401at6656\tMissing\n+138502at6656\tMissing\n+138553at6656\tMissing\n+138659at6656\tMissing\n+138684at6656\tMissing\n+138937at6656\tMissing\n+139217at6656\tMissing\n+139553at6656\tMissing\n+139638at6656\tMissing\n+139744at6656\tMissing\n+139834at6656\tMissing\n+140076at6656\tMissing\n+140197at6656\tMissing\n+140198at6656\tMissing\n+140403at6656\tMissing\n+140461at6656\tMissing\n+140693at6656\tMissing\n+140874at6656\tMissing\n+140903at6656\tMissing\n+141031at6656\tMissing\n+141163at6656\tMissing\n+141166at6656\tMissing\n+141175at6656\tMissing\n+141298at6656\tMissing\n+141804at6656\tMissing\n+141859at6656\tMissing\n+141916at6656\tMissing\n+142388at6656\tMissing\n+142415at6656\tMissing\n+142522at6656\tMissing\n+1426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|
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/proteome_results/missing_buscos_list --- a/test-data/proteome_results/missing_buscos_list Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/proteome_results/missing_buscos_list Mon Aug 17 06:50:18 2020 -0400 |
| b |
| b'@@ -1,4 +1,1015 @@\n-# BUSCO version is: 3.0.2 \n-# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A)\n-# 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\n-#\n+# BUSCO version is: 4.1.2 \n+# The lineage dataset is: arthropoda_odb10 (Creation date: 2019-11-20, number of species: 90, number of BUSCOs: 1013)\n+# Busco 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|
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/proteome_results/short_summary --- a/test-data/proteome_results/short_summary Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/proteome_results/short_summary Mon Aug 17 06:50:18 2020 -0400 |
| [ |
| @@ -1,15 +1,14 @@ -# 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 +# BUSCO version is: 4.1.2 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2019-11-20, number of species: 90, number of BUSCOs: 1013) +# Summarized benchmarking in BUSCO notation for file /tmp/tmpsafr8yho/files/5/e/9/dataset_5e95c1d5-37e1-4fca-8e9b-3058fa860695.dat # BUSCO was run in mode: proteins - C:0.0%[S:0.0%,D:0.0%],F:100.0%,M:0.0%,n:1 + ***** Results: ***** - 0 Complete BUSCOs (C) - 0 Complete and single-copy BUSCOs (S) - 0 Complete and duplicated BUSCOs (D) - 1 Fragmented BUSCOs (F) - 0 Missing BUSCOs (M) - 1 Total BUSCO groups searched + C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 + 1 Complete BUSCOs (C) + 1 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 1012 Missing BUSCOs (M) + 1013 Total BUSCO groups searched |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/transcriptome_results/full_table --- a/test-data/transcriptome_results/full_table Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/transcriptome_results/full_table Mon Aug 17 06:50:18 2020 -0400 |
| b |
| b'@@ -1,6 +1,1016 @@\n-# BUSCO version is: 3.0.2 \n-# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A)\n-# 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\n-#\n-# Busco id\tStatus\tSequence\tScore\tLength\n-BUSCOaEOG7B0HST\tMissing\n+# BUSCO version is: 4.1.2 \n+# The lineage dataset is: arthropoda_odb10 (Creation date: 2019-11-20, number of species: 90, number of BUSCOs: 1013)\n+# Busco id\tStatus\tSequence\tScore\tLength\tOrthoDB url\tDescription\n+774at6656\tMissing\n+980at6656\tMissing\n+997at6656\tMissing\n+1166at6656\tMissing\n+1885at6656\tMissing\n+1990at6656\tMissing\n+2148at6656\tMissing\n+2456at6656\tMissing\n+2473at6656\tMissing\n+3310at6656\tMissing\n+3585at6656\tMissing\n+3644at6656\tMissing\n+4136at6656\tMissing\n+4227at6656\tMissing\n+4864at6656\tMissing\n+5277at6656\tMissing\n+5616at6656\tMissing\n+6453at6656\tMissing\n+6563at6656\tMissing\n+6715at6656\tMissing\n+6820at6656\tMissing\n+7210at6656\tMissing\n+8145at6656\tMissing\n+8495at6656\tMissing\n+8847at6656\tMissing\n+8913at6656\tMissing\n+9647at6656\tMissing\n+9648at6656\tMissing\n+10240at6656\tMissing\n+10573at6656\tMissing\n+11384at6656\tMissing\n+12029at6656\tMissing\n+12174at6656\tMissing\n+12383at6656\tMissing\n+12771at6656\tMissing\n+12846at6656\tMissing\n+13019at6656\tMissing\n+13051at6656\tMissing\n+13736at6656\tMissing\n+13833at6656\tMissing\n+13858at6656\tMissing\n+13890at6656\tMissing\n+13934at6656\tMissing\n+14090at6656\tMissing\n+14257at6656\tMissing\n+14447at6656\tMissing\n+14995at6656\tMissing\n+15200at6656\tMissing\n+15697at6656\tMissing\n+15905at6656\tMissing\n+16061at6656\tMissing\n+16084at6656\tMissing\n+16220at6656\tMissing\n+16630at6656\tMissing\n+16648at6656\tMissing\n+17096at6656\tMissing\n+17122at6656\tMissing\n+17128at6656\tMissing\n+17748at6656\tMissing\n+18036at6656\tMissing\n+18055at6656\tMissing\n+18073at6656\tMissing\n+18630at6656\tMissing\n+18929at6656\tMissing\n+19044at6656\tMissing\n+19058at6656\tMissing\n+19104at6656\tMissing\n+19129at6656\tMissing\n+19208at6656\tMissing\n+19289at6656\tMissing\n+19590at6656\tMissing\n+19760at6656\tMissing\n+20093at6656\tMissing\n+20162at6656\tMissing\n+20267at6656\tMissing\n+20935at6656\tMissing\n+20936at6656\tMissing\n+21019at6656\tMissing\n+21191at6656\tMissing\n+21361at6656\tMissing\n+21367at6656\tMissing\n+21385at6656\tMissing\n+22098at6656\tMissing\n+22148at6656\tMissing\n+22358at6656\tMissing\n+22364at6656\tComplete\tBUSCOaEOG7B0HST\t1355.6\t788\thttps://www.orthodb.org/v10?query=22364at6656\timportin-5\n+22468at6656\tMissing\n+22611at6656\tMissing\n+22887at6656\tMissing\n+23309at6656\tMissing\n+23388at6656\tMissing\n+23429at6656\tMissing\n+23917at6656\tMissing\n+24255at6656\tMissing\n+24427at6656\tMissing\n+24459at6656\tMissing\n+24556at6656\tMissing\n+24573at6656\tMissing\n+25554at6656\tMissing\n+25680at6656\tMissing\n+26078at6656\tMissing\n+26653at6656\tMissing\n+26734at6656\tMissing\n+27198at6656\tMissing\n+27515at6656\tMissing\n+27617at6656\tMissing\n+27655at6656\tMissing\n+28325at6656\tMissing\n+28380at6656\tMissing\n+28519at6656\tMissing\n+28685at6656\tMissing\n+28872at6656\tMissing\n+29213at6656\tMissing\n+29237at6656\tMissing\n+29365at6656\tMissing\n+29730at6656\tMissing\n+29744at6656\tMissing\n+30156at6656\tMissing\n+30184at6656\tMissing\n+30267at6656\tMissing\n+30463at6656\tMissing\n+30512at6656\tMissing\n+30526at6656\tMissing\n+30642at6656\tMissing\n+30822at6656\tMissing\n+30918at6656\tMissing\n+30962at6656\tMissing\n+31014at6656\tMissing\n+31119at6656\tMissing\n+31196at6656\tMissing\n+31333at6656\tMissing\n+31480at6656\tMissing\n+31615at6656\tMissing\n+31634at6656\tMissing\n+31820at6656\tMissing\n+31886at6656\tMissing\n+31919at6656\tMissing\n+32694at6656\tMissing\n+32733at6656\tMissing\n+32851at6656\tMissing\n+33187at6656\tMissing\n+33566at6656\tMissing\n+33794at6656\tMissing\n+34586at6656\tMissing\n+34917at6656\tMissing\n+35035at6656\tMissing\n+35548at6656\tMissing\n+35680at6656\tMissing\n+35708at6656\tMissing\n+35995at6656\tMissing\n+36374at6656\tMissing\n+36387at6656\tMissing\n+36403at6656\tMissing\n+36463at6656\tMissing\n+37030at6656\tMissing'..b'90at6656\tMissing\n+135702at6656\tMissing\n+135764at6656\tMissing\n+135828at6656\tMissing\n+135834at6656\tMissing\n+135859at6656\tMissing\n+135975at6656\tMissing\n+135994at6656\tMissing\n+136055at6656\tMissing\n+136095at6656\tMissing\n+136119at6656\tMissing\n+136224at6656\tMissing\n+136365at6656\tMissing\n+136559at6656\tMissing\n+136888at6656\tMissing\n+137050at6656\tMissing\n+137197at6656\tMissing\n+137202at6656\tMissing\n+137334at6656\tMissing\n+137338at6656\tMissing\n+137422at6656\tMissing\n+137609at6656\tMissing\n+137688at6656\tMissing\n+137709at6656\tMissing\n+137711at6656\tMissing\n+138243at6656\tMissing\n+138271at6656\tMissing\n+138379at6656\tMissing\n+138401at6656\tMissing\n+138502at6656\tMissing\n+138553at6656\tMissing\n+138659at6656\tMissing\n+138684at6656\tMissing\n+138937at6656\tMissing\n+139217at6656\tMissing\n+139553at6656\tMissing\n+139638at6656\tMissing\n+139744at6656\tMissing\n+139834at6656\tMissing\n+140076at6656\tMissing\n+140197at6656\tMissing\n+140198at6656\tMissing\n+140403at6656\tMissing\n+140461at6656\tMissing\n+140693at6656\tMissing\n+140874at6656\tMissing\n+140903at6656\tMissing\n+141031at6656\tMissing\n+141163at6656\tMissing\n+141166at6656\tMissing\n+141175at6656\tMissing\n+141298at6656\tMissing\n+141804at6656\tMissing\n+141859at6656\tMissing\n+141916at6656\tMissing\n+142388at6656\tMissing\n+142415at6656\tMissing\n+142522at6656\tMissing\n+142613at6656\tMissing\n+142661at6656\tMissing\n+142833at6656\tMissing\n+143154at6656\tMissing\n+143279at6656\tMissing\n+143459at6656\tMissing\n+143489at6656\tMissing\n+143562at6656\tMissing\n+143626at6656\tMissing\n+143709at6656\tMissing\n+143812at6656\tMissing\n+143930at6656\tMissing\n+144337at6656\tMissing\n+144652at6656\tMissing\n+144836at6656\tMissing\n+144851at6656\tMissing\n+144853at6656\tMissing\n+145033at6656\tMissing\n+145102at6656\tMissing\n+145443at6656\tMissing\n+145610at6656\tMissing\n+145811at6656\tMissing\n+145996at6656\tMissing\n+146007at6656\tMissing\n+146036at6656\tMissing\n+146087at6656\tMissing\n+146102at6656\tMissing\n+146103at6656\tMissing\n+146383at6656\tMissing\n+146600at6656\tMissing\n+146920at6656\tMissing\n+147002at6656\tMissing\n+147025at6656\tMissing\n+147322at6656\tMissing\n+147657at6656\tMissing\n+147723at6656\tMissing\n+147852at6656\tMissing\n+147891at6656\tMissing\n+147980at6656\tMissing\n+148134at6656\tMissing\n+148619at6656\tMissing\n+148713at6656\tMissing\n+148851at6656\tMissing\n+148890at6656\tMissing\n+149101at6656\tMissing\n+149126at6656\tMissing\n+149251at6656\tMissing\n+149405at6656\tMissing\n+149680at6656\tMissing\n+149753at6656\tMissing\n+149796at6656\tMissing\n+149819at6656\tMissing\n+149973at6656\tMissing\n+149977at6656\tMissing\n+150005at6656\tMissing\n+150049at6656\tMissing\n+150137at6656\tMissing\n+150182at6656\tMissing\n+150251at6656\tMissing\n+150327at6656\tMissing\n+150479at6656\tMissing\n+150583at6656\tMissing\n+150585at6656\tMissing\n+150667at6656\tMissing\n+150765at6656\tMissing\n+151102at6656\tMissing\n+151111at6656\tMissing\n+151114at6656\tMissing\n+151393at6656\tMissing\n+151436at6656\tMissing\n+151642at6656\tMissing\n+151658at6656\tMissing\n+152032at6656\tMissing\n+152109at6656\tMissing\n+152402at6656\tMissing\n+152534at6656\tMissing\n+152871at6656\tMissing\n+153155at6656\tMissing\n+153232at6656\tMissing\n+153312at6656\tMissing\n+153534at6656\tMissing\n+153693at6656\tMissing\n+153873at6656\tMissing\n+154133at6656\tMissing\n+154415at6656\tMissing\n+154507at6656\tMissing\n+155285at6656\tMissing\n+156057at6656\tMissing\n+156081at6656\tMissing\n+156111at6656\tMissing\n+156305at6656\tMissing\n+156395at6656\tMissing\n+156728at6656\tMissing\n+156824at6656\tMissing\n+156882at6656\tMissing\n+156975at6656\tMissing\n+157486at6656\tMissing\n+157579at6656\tMissing\n+157851at6656\tMissing\n+157879at6656\tMissing\n+158194at6656\tMissing\n+158760at6656\tMissing\n+159231at6656\tMissing\n+159420at6656\tMissing\n+159542at6656\tMissing\n+160675at6656\tMissing\n+160705at6656\tMissing\n+161435at6656\tMissing\n+162059at6656\tMissing\n+162147at6656\tMissing\n+162594at6656\tMissing\n+162628at6656\tMissing\n+162841at6656\tMissing\n+163670at6656\tMissing\n+163896at6656\tMissing\n+164354at6656\tMissing\n+164512at6656\tMissing\n+165142at6656\tMissing\n+165207at6656\tMissing\n+165493at6656\tMissing\n+166476at6656\tMissing\n+166479at6656\tMissing\n+166485at6656\tMissing\n+169220at6656\tMissing\n' |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/transcriptome_results/missing_buscos_list --- a/test-data/transcriptome_results/missing_buscos_list Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/transcriptome_results/missing_buscos_list Mon Aug 17 06:50:18 2020 -0400 |
| b |
| b'@@ -1,5 +1,1015 @@\n-# BUSCO version is: 3.0.2 \n-# The lineage dataset is: N/A (Creation date: N/A, number of species: N/A, number of BUSCOs: N/A)\n-# 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\n-#\n-BUSCOaEOG7B0HST\n+# BUSCO version is: 4.1.2 \n+# The lineage dataset is: arthropoda_odb10 (Creation date: 2019-11-20, number of species: 90, number of BUSCOs: 1013)\n+# Busco 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|
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 test-data/transcriptome_results/short_summary --- a/test-data/transcriptome_results/short_summary Wed Dec 04 13:45:35 2019 -0500 +++ b/test-data/transcriptome_results/short_summary Mon Aug 17 06:50:18 2020 -0400 |
| [ |
| @@ -1,15 +1,14 @@ -# 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 version is: 4.1.2 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2019-11-20, number of species: 90, number of BUSCOs: 1013) +# Summarized benchmarking in BUSCO notation for file /tmp/tmpsafr8yho/files/9/9/2/dataset_9922e6bd-50c2-4b64-8e36-70b9b9c3f8ed.dat # BUSCO was run in mode: transcriptome - C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:1 + ***** Results: ***** - 0 Complete BUSCOs (C) - 0 Complete and single-copy BUSCOs (S) - 0 Complete and duplicated BUSCOs (D) - 0 Fragmented BUSCOs (F) - 1 Missing BUSCOs (M) - 1 Total BUSCO groups searched + C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 + 1 Complete BUSCOs (C) + 1 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 1012 Missing BUSCOs (M) + 1013 Total BUSCO groups searched |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 tool-data/busco.loc.sample --- a/tool-data/busco.loc.sample Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,18 +0,0 @@ -# This is a sample file distributed with Galaxy that is used to define a -# list of busco datasets, using four columns tab separated: -# -# <unique_build_id> <display_name> <genome_fasta_file_path> -# -# Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html -# -# "/some/path/datasets/" would be the last column in the line -# If this were for the /some/path/lineage/cyanobacteria_odb9/ reference dataset: -# -# $ ls /some/path/datasets/cyanobacteria_odb9/ -# ancestral ancestral_variants dataset.cfg hmms info lengths_cutoff prfl scores_cutoff -# -# the resulting entry would look like: -# -#cyanobacteria_odb9 cyanobacteria /some/path/datasets/ -# -# |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<tables> - <table name="busco" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/busco.loc" /> - </table> -</tables> |
| b |
| diff -r 1e62c28ba91d -r 4048d82f0c88 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Wed Dec 04 13:45:35 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ -<tables> - <table name="busco" comment_char="#"> - <columns>value, name, path</columns> - <file path="${__HERE__}/test-data/busco.loc" /> - </table> -</tables> |