| Previous changeset 1:87983967544b (2017-01-24) Next changeset 3:f18f0b887c31 (2018-12-14) |
|
Commit message:
planemo upload commit 2896dcfd180800d00ea413a59264ef8b11788b8e |
|
modified:
busco.xml test-data/busco.loc 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 tool-data/busco.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
|
added:
test-data/local.tar.gz |
| b |
| 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 |
| [ |
| b'@@ -1,22 +1,39 @@\n-<tool id="busco" name="Busco" version="2.0">\n+<tool id="busco" name="Busco" version="3.0.2">\n <description>assess genome assembly and annotation completeness</description>\n-\n <requirements>\n- <requirement type="package" version="2.0">busco</requirement>\n+ <requirement type="package" version="3.0.2">busco</requirement>\n+ <requirement type="package" version="2.2.1">r-ggplot2</requirement>\n </requirements>\n+ <command><![CDATA[\n+ export BUSCO_CONFIG_FILE=\'busco_config.ini\'\n \n- <command><![CDATA[\n- BUSCO.py\n+ &&\n+\n+ #if $adv.aug_prediction.augustus_mode == \'history\':\n+ ## Using an augustus model from history, we need to unzip it and let augustus find it\n+\n+ cp -r "\\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&\n+\n+ mkdir -p \'augustus_dir/species/\' &&\n+\n+ tar -C \'augustus_dir/species/\' -xzvf \'${adv.aug_prediction.augustus_model}\' > /dev/null &&\n+\n+ export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&\n+ #end if\n+\n+ run_BUSCO.py\n --in \'${input}\'\n- --lineage \'${lineage.fields.path}\'\n+ --lineage_path \'${lineage_path.fields.path}/${lineage_path.fields.value}\'\n --mode \'${mode}\'\n -o "busco_galaxy"\n --cpu \\${GALAXY_SLOTS:-4}\n --evalue ${adv.evalue}\n ${adv.long}\n --limit ${adv.limit}\n- #if $adv.species:\n- --species \'${adv.species}\'\n+ #if $adv.aug_prediction.augustus_mode == \'builtin\':\n+ --species \'${adv.aug_prediction.augustus_species}\'\n+ #else if $adv.aug_prediction.augustus_mode == \'history\':\n+ --species local\n #end if\n --tarzip\n ]]></command>\n@@ -24,14 +41,13 @@\n <inputs>\n \n <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />\n-\n <param argument="--mode" type="select" label="Mode">\n <option value="geno">Genome</option>\n <option value="tran">Transcriptome</option>\n <option value="prot">Proteome</option>\n </param>\n \n- <param argument="--lineage" type="select" label="Lineage">\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@@ -41,7 +57,118 @@\n <section name="adv" title="Advanced Options" expanded="False">\n <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>\n <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>\n- <param argument="--species" type="text" optional="True" label="Name of existing Augustus species gene finding metaparameters"/>\n+\n+ <conditional name="aug_prediction">\n+ <param name="augustus_mode" type="select" label="Augustus species model">\n+ <option value="no" selected="true">Use the default species for selected lineage</option>\n+ <option value="builtin">Use another predefined species model</option>\n+ <option value="history">Use a custom species model</option>\n+ </param>\n+ <when value="no"/>\n+ <when value="history">\n+ <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>\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="'..b'ns1">maker2_c_elegans1</option>\n+ <option value="maker2_dmel1">maker2_dmel1</option>\n+ <option value="maker2_spomb1">maker2_spomb1</option>\n+ <option value="parasteatoda">parasteatoda</option>\n+ <option value="rice">rice</option>\n+ <option value="schistosoma2">schistosoma2</option>\n+ <option value="sulfolobus_solfataricus">sulfolobus_solfataricus</option>\n+ </param>\n+ </when>\n+ </conditional>\n <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>\n </section>\n </inputs>\n@@ -53,7 +180,7 @@\n <tests>\n <test>\n <param name="input" value="genome.fa"/>\n- <param name="lineage" value="arthropoda_2.0"/>\n+ <param name="lineage_path" value="arthropoda"/>\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@@ -61,7 +188,7 @@\n </test>\n <test>\n <param name="input" value="proteome.fa"/>\n- <param name="lineage" value="arthropoda_2.0"/>\n+ <param name="lineage_path" value="arthropoda"/>\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@@ -69,12 +196,32 @@\n </test>\n <test>\n <param name="input" value="transcriptome.fa"/>\n- <param name="lineage" value="arthropoda_2.0"/>\n+ <param name="lineage_path" value="arthropoda"/>\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 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>\n </test>\n+ <test>\n+ <param name="input" value="genome.fa"/>\n+ <param name="lineage_path" value="arthropoda"/>\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+ <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+ <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>\n+ </test>\n+ <test>\n+ <param name="input" value="genome.fa"/>\n+ <param name="lineage_path" value="arthropoda"/>\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+ <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+ <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>\n+ </test>\n </tests>\n <help>\n BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs\n' |
| b |
| 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 |
| b |
| @@ -1,1 +1,1 @@ -arthropoda_2.0 arthropoda_2.0 Arthropoda (v2) ${__HERE__}/arthropoda/ +arthropoda Arthropoda data ${__HERE__}/ |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| diff -r 87983967544b -r 382a4c19007f test-data/local.tar.gz |
| b |
| Binary file test-data/local.tar.gz has changed |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 # |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| 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 |
| b |
| @@ -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: # -# <unique_build_id> <dbkey> <display_name> <genome_fasta_file_path> +# <unique_build_id> <display_name> <genome_fasta_file_path> # # 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/ # # |
| b |
| 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 |
| b |
| @@ -1,6 +1,6 @@ <tables> <table name="busco" comment_char="#"> - <columns>value, dbkey, name, path</columns> + <columns>value, name, path</columns> <file path="tool-data/busco.loc" /> </table> </tables> |
| b |
| 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 |
| b |
| @@ -1,6 +1,6 @@ <tables> <table name="busco" comment_char="#"> - <columns>value, dbkey, name, path</columns> + <columns>value, name, path</columns> <file path="${__HERE__}/test-data/busco.loc" /> </table> </tables> |