Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/3.0.3+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/nml/mob_suite/mob_recon/1.4.1 |
mob_recon |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
mob_suite | 3.0.3 | package |
Additional information about this tool |
#import re #import os.path #set $named_input = re.sub(r'(\s|\(|\)|:|!)', '_', str($input.element_identifier)+'.fasta') ln -s '$input' '$named_input' && mob_recon --num_threads \${GALAXY_SLOTS:-4} --infile '${named_input}' --run_typer #if $adv_param.unicycler_contigs: --unicycler_contigs #end if #if $adv_param.run_overhang: --run_overhang #end if #if $adv_param.debug: --debug #end if #if $adv_param.plasmid_db --plasmid_db '$adv_param.plasmid_db' #end if #if $adv_param.plasmid_mash_db --plasmid_mash_db '$adv_param.plasmid_mash_db' #end if #if $adv_param.plasmid_meta --plasmid_meta '$adv_param.plasmid_meta' #end if #if $adv_param.repetitive_mask --repetitive_mask '$adv_param.repetitive_mask' #end if #if $adv_param.plasmid_mob --plasmid_mob '$adv_param.plasmid_mob' #end if #if $adv_param.plasmid_mpf --plasmid_mpf '$adv_param.plasmid_mpf' #end if #if $adv_param.plasmid_orit --plasmid_orit '$adv_param.plasmid_orit' #end if --min_length '${adv_param.min_length}' --min_rep_evalue '${adv_param.min_rep_evalue}' --min_rep_evalue '${adv_param.min_rep_evalue}' --min_mob_evalue '${adv_param.min_mob_evalue}' --min_con_evalue '${adv_param.min_con_evalue}' --min_rep_ident '${adv_param.min_rep_ident}' --min_mob_ident '${adv_param.min_mob_ident}' --min_con_ident '${adv_param.min_con_ident}' --min_rpp_ident '${adv_param.min_rpp_ident}' --min_rep_cov '${adv_param.min_rep_cov}' --min_mob_cov '${adv_param.min_mob_cov}' --min_con_cov '${adv_param.min_con_cov}' --min_rpp_cov '${adv_param.min_rpp_cov}' --outdir 'outdir' && mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true)
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input: Ecoli_strain_KV7_complete_LT795502.fasta adv_param|unicycler_contigs: True adv_param|run_overhang: True |
name: value name: value |
Ecoli_strain_KV7_complete_LT795502.fasta value |