| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/deeparg_short_reads/deeparg_short_reads/1.0.4+galaxy0 (this tool) |
| deeparg_short_reads |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| deeparg | 1.0.4 | package |
| trimmomatic | 0.39 | package |
| vsearch | 2.27.1 | package |
| bowtie2 | 2.3.5.1 | package |
| bedtools | 2.29.2 | package |
| samtools | 1.3.1 | package |
| Additional information about this tool |
## Used only for test
#if str($hide_db_build) == 'true':
deeparg download_data -o '$deeparg_db.fields.path' &&
#end if
##
mkdir -p deeparg_short_reads_output &&
#set $extension = str($forward_pe_file.ext)
ln -s -f '${forward_pe_file}' 'input_forward.${extension}' &&
#set $extension = str($reverse_pe_file.ext)
ln -s -f '${reverse_pe_file}' 'input_reverse.${extension}' &&
deeparg short_reads_pipeline
--forward_pe_file 'input_forward.${extension}'
--reverse_pe_file 'input_reverse.${extension}'
--output_file 'deeparg_short_reads_output/SR'
-d '$deeparg_db.fields.path'
--deeparg_identity $deeparg_identity
--deeparg_probability $deeparg_probability
--deeparg_evalue $deeparg_evalue
--gene_coverage $gene_coverage
--bowtie_16s_identity $bowtie_16s_identity
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
hide_db_build: true forward_pe_file: light_F.fq.gz reverse_pe_file: light_R.fq.gz deeparg_db: deeparg_1.0.4-19122024 output_files|output_selection: ['file_ARG_tsv', 'file_merged_ARG_tsv', 'file_ARG_subtype_tsv', 'file_ARG_type_tsv', 'file_potential_ARG_tsv', 'file_all_hits_tsv'] |
name: value name: value name: value name: value name: value name: value |
light_F.fq.gz light_R.fq.gz value |