Batch file format (draft)

Template

A tabulate file without constraint on number of columns. A job per line. The first column must be the job type. Each job parameter has a key=value syntax. Apart first column, order has no importance

Align job

type=align target=<target_url> query=<query_url> tool=<tool_id> options=<options_id1>,<options_id2> ...

Mandatory:

• type=align
• target

Optional:

• job_id_prefix
• query
• options

For option part, options_id are separate by coma. They look like 0-0 for 1st choice of 1st option, 0-1 for 2nd choice of 1st option, ..., 1-0 for 1nd choice of 2nd option, ... If options are not precised, default ones will be use. In case of checkbox, the option_id can be negate by using this syntax !options_id

The mapping between options_id and its meaning will be displayed on batch page.

Plot job

Two possible patterns:

type=plot align=<paf_url> target=<target_url> query=<query_url>
type=plot backup="<backup_url>"

Mandatory:

• type=plot
• exclusive:
  • backup
  • align, target and query

Optional:

• job_id_prefix

Example

align tool=minimap2 options=0-0 query=http://ftp.ensemblgenomes.org/pub/bacteria/release-52/fasta/bacteria_79_collection/escherichia_coli_str_k_12_substr_w3110_gca_000010245/dna/Escherichia_coli_str_k_12_substr_w3110_gca_000010245.ASM1024v1.dna_rm.toplevel.fa.gz target=http://ftp.ensemblgenomes.org/pub/bacteria/release-52/fasta/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/dna/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.dna_rm.toplevel.fa.gz
align tool=minimap2 options=0-0	query=http://ftp.ensemblgenomes.org/pub/bacteria/release-52/fasta/bacteria_22_collection/escherichia_coli_o157_h7_gca_004100305/dna/Escherichia_coli_o157_h7_gca_004100305.ASM410030v1.dna_rm.toplevel.fa.gz target=http://ftp.ensemblgenomes.org/pub/bacteria/release-52/fasta/bacteria_0_collection/escherichia_coli_str_k_12_substr_mg1655_gca_000005845/dna/Escherichia_coli_str_k_12_substr_mg1655_gca_000005845.ASM584v2.dna_rm.toplevel.fa.gz
align tool=minimap2 options=0-0 query=http://ftp.ensemblgenomes.org/pub/bacteria/release-52/fasta/bacteria_22_collection/escherichia_coli_o157_h7_gca_004100305/dna/Escherichia_coli_o157_h7_gca_004100305.ASM410030v1.dna_rm.toplevel.fa.gz target=http://ftp.ensemblgenomes.org/pub/bacteria/release-52/fasta/bacteria_79_collection/escherichia_coli_str_k_12_substr_w3110_gca_000010245/dna/Escherichia_coli_str_k_12_substr_w3110_gca_000010245.ASM1024v1.dna_rm.toplevel.fa.gz