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view mob_recon.xml @ 5:09424ec94e80 draft
"planemo upload for repository https://github.com/phac-nml/mob-suite commit e3f242a0dbf429ac0394b6962441aaef367645a8"
author | nml |
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date | Wed, 13 Nov 2019 14:09:11 -0500 |
parents | 1c5dfecfbb4d |
children | 9424de64bfa8 |
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<tool id="mob_recon" name="MOB-Recon" version="1.4.9.1+galaxy0"> <description>Type contigs and extract plasmid sequences</description> <requirements> <requirement type="package" version="1.4.9.1">mob_suite</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ #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}" #if str($adv_param.unicycler_contigs) == "True": --unicycler_contigs #end if #if str($adv_param.run_circlator) == "True": --run_circlator #end if #if str($adv_param.min_length_condition.min_length_param) == "True": --min_length ${adv_param.min_length_condition.min_length_value} #end if --run_typer --min_rep_evalue '${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}' --outdir '.' && mkdir ./sequences && (cp plasmid*.fasta chromosome.fasta ./sequences 2> /dev/null || true) ]]> </command> <inputs> <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> <section name="adv_param" title="Advanced parameters" expanded="False"> <param name="unicycler_contigs" label="Check for circularity flag generated by unicycler in contigs fasta headers" type="select" value="True"> <option value="True">Yes</option> <option value="False">No</option> </param> <param name="run_circlator" label="Run circlator minums2 pipeline to check for circular contigs" type="select" value="True"> <option value="True">Yes</option> <option value="False">No</option> </param> <conditional name="min_length_condition"> <param name="min_length_param" label="Minimum length of contigs to process" type="select" value="False"> <option value="False">No</option> <option value="True">Yes</option> </param> <when value="True"> <param name="min_length_value" type="integer" value="500" min="50"/> </when> <when value="False"/> </conditional> <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001"/> <param name="min_mob_evalue" label="Minimum evalue threshold for relaxase tblastn" type="float" min="0.00001" max="1" value="0.00001"/> <param name="min_con_evalue" label="Minimum evalue threshold for contig blastn" type="float" min="0.00001" max="1" value="0.00001"/> <param name="min_rpp_evalue" label="Minimum evalue threshold for repetitve elements blastn" type="float" min="0.00001" max="1" value="0.00001"/> <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/> <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/> <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/> <param name="min_rpp_ident" label="Minimum sequence identity for repetitive elements" type="integer" min="0" max="100" value="80"/> </section> </inputs> <outputs> <data name="outfile1" format="tabular" from_work_dir="contig_report.txt" label="${tool.name} on ${on_string}: Overall contig MOB-recon report"/> <data name="outfile2" format="tabular" from_work_dir="repetitive_blast_report.txt" label="${tool.name} on ${on_string}: Repetitive elements BLAST report"/> <data name="outfile3" format="tabular" from_work_dir="mobtyper_aggregate_report.txt" label="${tool.name} on ${on_string}: Aggregate MOB-typer report for all contigs"/> <collection name="seqhits" type="list" label="${tool.name} on ${on_string}: Extracted sequences (plasmids,chromosome(s))"> <discover_datasets pattern="__name_and_ext__" directory="sequences" /> </collection> </outputs> <tests> <test> <param name="input" value="plasmid_476.fasta" ftype="fasta"/> <section name="adv_param"> <param name="unicycler_contigs" value="True"/> <param name="run_circlator" value="True"/> </section> <output name="outfile1"> <assert_contents> <has_text text="NC_019097"/> </assert_contents> </output> </test> </tests> <help> **Syntax** This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases. For more information please visit https://github.com/phac-nml/mob-suite/. **Workflow** This preliminary \"Mobilome and Resistome Analysis Workflow\" linking mob_recon with staramr provides reports on mobilome and resistome for a given isolate given a draft genome assembly. The workflow is located in Shared Data --> Workflows --> Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR). The workflow file can also be manually downloaded from https://raw.githubusercontent.com/phac-nml/galaxy_tools/master/tools/mob_suite/workflows/AMRworkflow_STARAMR.ga. ----- **Input:** A FASTA file with a single or multiple contigs (e.g. a draft genome assembly): **Output:** Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column. Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome. </help> <citations> <citation type="bibtex"> @misc{githubmob-suite, author = {Robertson J, Nash J}, title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.}, publisher = {GitHub}, journal = {GitHub repository}, doi = {10.1099/mgen.0.000206}, url = {https://github.com/phac-nml/mob-suite} }</citation> </citations> </tool>