| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/checkm_qa/checkm_qa/1.2.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/checkm_qa/checkm_qa/1.2.4+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/checkm_qa/checkm_qa/1.2.4+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/checkm_qa/checkm_qa/1.2.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/checkm_qa/checkm_qa/1.2.3+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/checkm_qa/checkm_qa/1.2.0+galaxy0 |
| checkm_qa |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| checkm-genome | 1.2.4 | package |
| Additional information about this tool |
#import re
mkdir -p 'output/storage/' &&
cp '$checkm_hmm_info' 'output/storage/checkm_hmm_info.pkl.gz' &&
cp '$bin_stats_analyze' 'output/storage/bin_stats.analyze.tsv' &&
#for $i in $hmmer_analyze
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
mkdir -p 'output/bins/${identifier}' &&
cp '$i' 'output/bins/${identifier}/hmmer.analyze.txt' &&
#end for
#if $output.out_format == '9'
#for $i in $output.genes_faa
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
mkdir -p 'output/bins/${identifier}' &&
cp '$i' 'output/bins/${identifier}/genes.faa' &&
#end for
#end if
checkm qa
'$marker_file'
'output'
--out_format $output.out_format
--tab_table
--file 'output_file'
#if $exclude_markers
--exclude_markers '$exclude_markers'
#end if
$individual_markers
$skip_adj_correction
$skip_pseudogene_correction
--aai_strain $aai_strain
$ignore_thresholds
--e_value $e_value
--length $length
#if $coverage
--coverage_file '$coverage'
#end if
--threads \${GALAXY_SLOTS:-1}
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
marker_file: lineage_marker_set checkm_hmm_info: checkm_hmm_info.pkl.gz bin_stats_analyze: bin_stats.analyze.tsv hmmer_analyze: list collection output|out_format: 1 individual_markers: False skip_adj_correction: False skip_pseudogene_correction: False aai_strain: 0.9 ignore_thresholds: False e_value: 1e-10 length: 0.7 extra_outputs: marker_gene_stats |
name: value name: value name: value |
lineage_marker_set checkm_hmm_info.pkl.gz bin_stats.analyze.tsv hmmer.analyze.txt value |
| Test-2 |
marker_file: lineage_marker_set checkm_hmm_info: checkm_hmm_info.pkl.gz bin_stats_analyze: bin_stats.analyze.tsv hmmer_analyze: list collection output|out_format: 2 individual_markers: False skip_adj_correction: False skip_pseudogene_correction: False aai_strain: 0.9 ignore_thresholds: False e_value: 1e-10 length: 0.7 |
name: value name: value |
lineage_marker_set checkm_hmm_info.pkl.gz bin_stats.analyze.tsv hmmer.analyze.txt value |
| Test-3 |
marker_file: lineage_marker_set checkm_hmm_info: checkm_hmm_info.pkl.gz bin_stats_analyze: bin_stats.analyze.tsv hmmer_analyze: list collection output|out_format: 3 individual_markers: False skip_adj_correction: False skip_pseudogene_correction: False aai_strain: 0.9 ignore_thresholds: False e_value: 1e-10 length: 0.7 |
name: value name: value |
lineage_marker_set checkm_hmm_info.pkl.gz bin_stats.analyze.tsv hmmer.analyze.txt value |
| Test-4 |
marker_file: lineage_marker_set checkm_hmm_info: checkm_hmm_info.pkl.gz bin_stats_analyze: bin_stats.analyze.tsv hmmer_analyze: list collection output|out_format: 4 individual_markers: False skip_adj_correction: False skip_pseudogene_correction: False aai_strain: 0.9 ignore_thresholds: False e_value: 1e-10 length: 0.7 |
name: value name: value |
lineage_marker_set checkm_hmm_info.pkl.gz bin_stats.analyze.tsv hmmer.analyze.txt value |
| Test-5 |
marker_file: lineage_marker_set checkm_hmm_info: checkm_hmm_info.pkl.gz bin_stats_analyze: bin_stats.analyze.tsv hmmer_analyze: list collection output|out_format: 5 individual_markers: False skip_adj_correction: False skip_pseudogene_correction: False aai_strain: 0.9 ignore_thresholds: False e_value: 1e-10 length: 0.7 |
name: value name: value |
lineage_marker_set checkm_hmm_info.pkl.gz bin_stats.analyze.tsv hmmer.analyze.txt value |
| Test-6 |
marker_file: lineage_marker_set checkm_hmm_info: checkm_hmm_info.pkl.gz bin_stats_analyze: bin_stats.analyze.tsv hmmer_analyze: list collection output|out_format: 6 individual_markers: False skip_adj_correction: False skip_pseudogene_correction: False aai_strain: 0.9 ignore_thresholds: False e_value: 1e-10 length: 0.7 |
name: value name: value |
lineage_marker_set checkm_hmm_info.pkl.gz bin_stats.analyze.tsv hmmer.analyze.txt value |
| Test-7 |
marker_file: lineage_marker_set checkm_hmm_info: checkm_hmm_info.pkl.gz bin_stats_analyze: bin_stats.analyze.tsv hmmer_analyze: list collection output|out_format: 7 individual_markers: False skip_adj_correction: False skip_pseudogene_correction: False aai_strain: 0.9 ignore_thresholds: False e_value: 1e-10 length: 0.7 |
name: value name: value |
lineage_marker_set checkm_hmm_info.pkl.gz bin_stats.analyze.tsv hmmer.analyze.txt value |
| Test-8 |
marker_file: lineage_marker_set checkm_hmm_info: checkm_hmm_info.pkl.gz bin_stats_analyze: bin_stats.analyze.tsv hmmer_analyze: list collection output|out_format: 8 individual_markers: False skip_adj_correction: False skip_pseudogene_correction: False aai_strain: 0.9 ignore_thresholds: False e_value: 1e-10 length: 0.7 |
name: value name: value |
lineage_marker_set checkm_hmm_info.pkl.gz bin_stats.analyze.tsv hmmer.analyze.txt value |
| Test-9 |
marker_file: lineage_marker_set checkm_hmm_info: checkm_hmm_info.pkl.gz bin_stats_analyze: bin_stats.analyze.tsv hmmer_analyze: list collection output|genes_faa: list collection output|out_format: 9 exclude_markers: markers_to_exclude individual_markers: False skip_adj_correction: False skip_pseudogene_correction: False aai_strain: 0.9 ignore_thresholds: False e_value: 1e-10 length: 0.7 |
name: value name: value |
lineage_marker_set checkm_hmm_info.pkl.gz bin_stats.analyze.tsv hmmer.analyze.txt 637000110.faa markers_to_exclude value |