| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.9+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.8.5.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/tooldistillator/tooldistillator/0.8.4.1+galaxy0 |
| tooldistillator |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| tooldistillator | 0.9 | package |
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
tool_section|tools_0|select_tool|input: abricate/report.tsv tool_section|tools_0|select_tool|analysis_software_version: 1.0 tool_section|tools_0|select_tool|reference_database_version: 2.0 tool_section|tools_0|select_tool|tool_list: abricate log: True |
name: value |
abricate/report.tsv value |
| Test-2 |
tool_section|tools_0|select_tool|input: bakta/bakta.json tool_section|tools_0|select_tool|annotation_tabular_path: bakta/bakta_summary.txt tool_section|tools_0|select_tool|annotation_genbank_path: bakta/bakta_summary.txt tool_section|tools_0|select_tool|annotation_embl_path: bakta/bakta_summary.txt tool_section|tools_0|select_tool|contig_sequences_path: bakta/bakta_summary.txt tool_section|tools_0|select_tool|hypothetical_protein_path: bakta/bakta_summary.txt tool_section|tools_0|select_tool|hypothetical_tabular_path: bakta/bakta_summary.txt tool_section|tools_0|select_tool|summary_result_path: bakta/bakta_summary.txt tool_section|tools_0|select_tool|nucleotide_annotation_path: bakta/bakta_nucleotide_annotation.ffn tool_section|tools_0|select_tool|amino_acid_annotation_path: bakta/bakta_aminoacid.faa tool_section|tools_0|select_tool|gff_file_path: bakta/bakta_annotation.gff3 tool_section|tools_0|select_tool|analysis_software_version: 1.8.1 tool_section|tools_0|select_tool|reference_database_version: 5.0 tool_section|tools_0|select_tool|tool_list: bakta |
bakta/bakta.json bakta/bakta_summary.txt bakta/bakta_nucleotide_annotation.ffn bakta/bakta_aminoacid.faa bakta/bakta_annotation.gff3 |
|
| Test-3 |
tool_section|tools_0|select_tool|input: bakta/bakta.json tool_section|tools_0|select_tool|tool_list: bakta |
bakta/bakta.json |
|
| Test-4 |
tool_section|tools_0|select_tool|input: abricate/report.tsv tool_section|tools_0|select_tool|analysis_software_version: 1.0 tool_section|tools_0|select_tool|reference_database_version: 2.0 tool_section|tools_0|select_tool|tool_list: abricate tool_section|tools_1|select_tool|input: amrfinderplus/AMRFinderPlus_report.tsv tool_section|tools_1|select_tool|point_mutation_report_path: amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv tool_section|tools_1|select_tool|nucleotide_sequence_path: amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta tool_section|tools_1|select_tool|analysis_software_version: 3.11.26 tool_section|tools_1|select_tool|reference_database_version: v3.11-2023-04-17.1 tool_section|tools_1|select_tool|tool_list: amrfinderplus tool_section|tools_2|select_tool|input: bakta/bakta.json tool_section|tools_2|select_tool|annotation_tabular_path: bakta/bakta_annotation.tsv tool_section|tools_2|select_tool|annotation_genbank_path: bakta/bakta_gbff.gbff tool_section|tools_2|select_tool|annotation_embl_path: bakta/bakta_embl.embl tool_section|tools_2|select_tool|contig_sequences_path: bakta/bakta_contigs_sequences.fna tool_section|tools_2|select_tool|hypothetical_protein_path: bakta/bakta_hypothetical.faa tool_section|tools_2|select_tool|hypothetical_tabular_path: bakta/bakta_hypothetical.tsv tool_section|tools_2|select_tool|plot_file_path: bakta/bakta_plot.svg tool_section|tools_2|select_tool|summary_result_path: bakta/bakta_summary.txt tool_section|tools_2|select_tool|nucleotide_annotation_path: bakta/bakta_nucleotide_annotation.ffn tool_section|tools_2|select_tool|amino_acid_annotation_path: bakta/bakta_aminoacid.faa tool_section|tools_2|select_tool|gff_file_path: bakta/bakta_annotation.gff3 tool_section|tools_2|select_tool|analysis_software_version: 1.8.1 tool_section|tools_2|select_tool|reference_database_version: 5.0 tool_section|tools_2|select_tool|tool_list: bakta tool_section|tools_3|select_tool|input: bandage/bandage_info.txt tool_section|tools_3|select_tool|bandage_plot_path: bandage/bandage_plot.svg tool_section|tools_3|select_tool|analysis_software_version: 1.0 tool_section|tools_3|select_tool|reference_database_version: 1.0 tool_section|tools_3|select_tool|tool_list: bandage tool_section|tools_4|select_tool|input: bracken/bracken_report.tsv tool_section|tools_4|select_tool|analysis_software_version: 1.0 tool_section|tools_4|select_tool|reference_database_version: 1.0 tool_section|tools_4|select_tool|kraken_report_path: bracken/bracken_kraken_report.tsv tool_section|tools_4|select_tool|threshold: 1 tool_section|tools_4|select_tool|read_len: 100 tool_section|tools_4|select_tool|level: S tool_section|tools_4|select_tool|tool_list: bracken tool_section|tools_5|select_tool|input: bwa/aligned_R1.bam tool_section|tools_5|select_tool|paired_second_file_path: bwa/aligned_R1.bam tool_section|tools_5|select_tool|analysis_software_version: 2.2.1 tool_section|tools_5|select_tool|reference_database_version: tests/data/dummy/flye/assembly.fasta tool_section|tools_5|select_tool|tool_list: bwa tool_section|tools_6|select_tool|input: fastp/fastp_report.json tool_section|tools_6|select_tool|trimmed_forward_R1_path: fastp/trimmed_R1.fastq.gz tool_section|tools_6|select_tool|trimmed_reverse_R2_path: fastp/trimmed_R2.fastq.gz tool_section|tools_6|select_tool|html_report_path: fastp/fastp_report.html tool_section|tools_6|select_tool|analysis_software_version: 1.0 tool_section|tools_6|select_tool|reference_database_version: 1.0 tool_section|tools_6|select_tool|tool_list: fastp tool_section|tools_7|select_tool|input: fastqc/fastqc_report.txt tool_section|tools_7|select_tool|html_report_path: fastqc/fastqc_report.html tool_section|tools_7|select_tool|analysis_software_version: 0.12.1 tool_section|tools_7|select_tool|reference_database_version: tool_section|tools_7|select_tool|tool_list: fastqc tool_section|tools_8|select_tool|input: filtlong/filtered_sample.fastq.gz tool_section|tools_8|select_tool|analysis_software_version: 0.2.1 tool_section|tools_8|select_tool|reference_database_version: tool_section|tools_8|select_tool|tool_list: filtlong tool_section|tools_9|select_tool|input: flye/assembly.fasta tool_section|tools_9|select_tool|contig_graph_path: flye/assembly.gfa tool_section|tools_9|select_tool|tsv_file_path: flye/assembly_infos.tsv tool_section|tools_9|select_tool|analysis_software_version: 2.9.1 tool_section|tools_9|select_tool|reference_database_version: tool_section|tools_9|select_tool|tool_list: flye tool_section|tools_10|select_tool|input: integronfinder2/results.integrons tool_section|tools_10|select_tool|summary_file_path: integronfinder2/results.summary tool_section|tools_10|select_tool|analysis_software_version: 1.0 tool_section|tools_10|select_tool|reference_database_version: 1.0 tool_section|tools_10|select_tool|tool_list: integronfinder2 tool_section|tools_11|select_tool|input: isescan/results.tsv tool_section|tools_11|select_tool|summary_path: isescan/summary.tsv tool_section|tools_11|select_tool|annotation_path: isescan/annotation.gff tool_section|tools_11|select_tool|orf_fna_path: isescan/orf.fna tool_section|tools_11|select_tool|orf_faa_path: isescan/orf.faa tool_section|tools_11|select_tool|is_fna_path: isescan/is.fna tool_section|tools_11|select_tool|analysis_software_version: 1.0 tool_section|tools_11|select_tool|reference_database_version: 1.0 tool_section|tools_11|select_tool|tool_list: isescan tool_section|tools_12|select_tool|input: kraken2/taxonomy_report.tsv tool_section|tools_12|select_tool|seq_classification_file_path: kraken2/taxonomy_result.tsv tool_section|tools_12|select_tool|analysis_software_version: 1.0 tool_section|tools_12|select_tool|reference_database_version: 1.0 tool_section|tools_12|select_tool|tool_list: kraken2 tool_section|tools_13|select_tool|input: plasmidfinder/plasmidfinder_result.json tool_section|tools_13|select_tool|genome_hit_path: plasmidfinder/genome_hit.fasta tool_section|tools_13|select_tool|plasmid_hit_path: plasmidfinder/plasmid_hit.fasta tool_section|tools_13|select_tool|analysis_software_version: 1.0 tool_section|tools_13|select_tool|reference_database_version: 1.0 tool_section|tools_13|select_tool|tool_list: plasmidfinder tool_section|tools_14|select_tool|input: polypolish/polished_assembly.fasta tool_section|tools_14|select_tool|analysis_software_version: 0.2.1 tool_section|tools_14|select_tool|reference_database_version: tool_section|tools_14|select_tool|tool_list: polypolish tool_section|tools_15|select_tool|input: quast/quast_result.tsv tool_section|tools_15|select_tool|quast_html_path: quast/quast_report.html tool_section|tools_15|select_tool|analysis_software_version: 0.5.0 tool_section|tools_15|select_tool|reference_database_version: tool_section|tools_15|select_tool|tool_list: quast tool_section|tools_16|select_tool|input: recentrifuge/rcf_data.tsv tool_section|tools_16|select_tool|rcf_stat_path: recentrifuge/rcf_stat.tsv tool_section|tools_16|select_tool|rcf_html_path: recentrifuge/rcf_report.html tool_section|tools_16|select_tool|analysis_software_version: 1.0 tool_section|tools_16|select_tool|reference_database_version: 1.0 tool_section|tools_16|select_tool|tool_list: recentrifuge tool_section|tools_17|select_tool|input: refseqmasher/refsesqmasher.tsv tool_section|tools_17|select_tool|analysis_software_version: 1.0 tool_section|tools_17|select_tool|reference_database_version: 1.0 tool_section|tools_17|select_tool|tool_list: refseqmasher tool_section|tools_18|select_tool|input: shovill/contigs.fa tool_section|tools_18|select_tool|contig_graph_path: shovill/contigs.gfa tool_section|tools_18|select_tool|bam_file_path: shovill/alignment.bam tool_section|tools_18|select_tool|analysis_software_version: 1.0 tool_section|tools_18|select_tool|reference_database_version: 1.0 tool_section|tools_18|select_tool|tool_list: shovill tool_section|tools_19|select_tool|input: staramr/resfinder.tsv tool_section|tools_19|select_tool|mlst_file_path: staramr/mlst.tsv tool_section|tools_19|select_tool|plasmidfinder_file_path: staramr/plasmidfinder.tsv tool_section|tools_19|select_tool|pointfinder_file_path: staramr/pointfinder.tsv tool_section|tools_19|select_tool|setting_file_path: staramr/settings.txt tool_section|tools_19|select_tool|analysis_software_version: 1.0 tool_section|tools_19|select_tool|reference_database_version: 1.0 tool_section|tools_19|select_tool|tool_list: staramr tool_section|tools_20|select_tool|input: tabular_file/report.tsv tool_section|tools_20|select_tool|analysis_software_name: test_galaxy tool_section|tools_20|select_tool|analysis_software_version: 1.0 tool_section|tools_20|select_tool|reference_database_version: 1.0 tool_section|tools_20|select_tool|tool_list: tabular_file |
abricate/report.tsv amrfinderplus/AMRFinderPlus_report.tsv amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta bakta/bakta.json bakta/bakta_annotation.tsv bakta/bakta_gbff.gbff bakta/bakta_embl.embl bakta/bakta_contigs_sequences.fna bakta/bakta_hypothetical.faa bakta/bakta_hypothetical.tsv bakta/bakta_plot.svg bakta/bakta_summary.txt bakta/bakta_nucleotide_annotation.ffn bakta/bakta_aminoacid.faa bakta/bakta_annotation.gff3 bandage/bandage_info.txt bandage/bandage_plot.svg bracken/bracken_report.tsv bracken/bracken_kraken_report.tsv bwa/aligned_R1.bam bwa/aligned_R1.bam fastp/fastp_report.json fastp/trimmed_R1.fastq.gz fastp/trimmed_R2.fastq.gz fastp/fastp_report.html fastqc/fastqc_report.txt fastqc/fastqc_report.html filtlong/filtered_sample.fastq.gz flye/assembly.fasta flye/assembly.gfa flye/assembly_infos.tsv integronfinder2/results.integrons integronfinder2/results.summary isescan/results.tsv isescan/summary.tsv isescan/annotation.gff isescan/orf.fna isescan/orf.faa isescan/is.fna kraken2/taxonomy_report.tsv kraken2/taxonomy_result.tsv plasmidfinder/plasmidfinder_result.json plasmidfinder/genome_hit.fasta plasmidfinder/plasmid_hit.fasta polypolish/polished_assembly.fasta quast/quast_result.tsv quast/quast_report.html recentrifuge/rcf_data.tsv recentrifuge/rcf_stat.tsv recentrifuge/rcf_report.html refseqmasher/refsesqmasher.tsv shovill/contigs.fa shovill/contigs.gfa shovill/alignment.bam staramr/resfinder.tsv staramr/mlst.tsv staramr/plasmidfinder.tsv staramr/pointfinder.tsv staramr/settings.txt tabular_file/report.tsv |