Mercurial > repos > dfornika > mob_suite
changeset 31:1a22c8de4205 draft
planemo upload for repository https://github.com/phac-nml/mob-suite commit 0dd60ac52b9d34ee1f446182eda78cb8c01de6d1-dirty
author | dfornika |
---|---|
date | Tue, 24 Sep 2019 19:01:44 -0400 |
parents | 14d499c3fe1d |
children | aaec1fe5415f |
files | mob_recon.xml mob_typer_zipped.xml |
diffstat | 2 files changed, 82 insertions(+), 1 deletions(-) [+] |
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--- a/mob_recon.xml Tue Sep 24 12:53:25 2019 -0400 +++ b/mob_recon.xml Tue Sep 24 19:01:44 2019 -0400 @@ -34,7 +34,7 @@ --min_rpp_ident '${adv_param.min_rpp_ident}' --outdir '.' && mkdir ./plasmids && (cp plasmid*.fasta ./plasmids 2> /dev/null || true) && - zip -r plasmids.zip plasmids + tar -czf plasmids.tar.gz plasmids ]]> </command> <inputs>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mob_typer_zipped.xml Tue Sep 24 19:01:44 2019 -0400 @@ -0,0 +1,81 @@ +<tool id="mob_typer" name="MOB-Typer" version="2.0.0"> + <description>Get the plasmid type and mobility given its sequence</description> + <requirements> + <requirement type="package" version="2.0.0">mob_suite</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + tar -xzf "${input}" && + mob_typer --num_threads \${GALAXY_SLOTS:-4} --infile "${input.name}" + --min_rep_evalue '$adv_param.min_rep_evalue_value' + --min_mob_evalue '$adv_param.min_mob_evalue_value' + --min_con_evalue '$adv_param.min_con_evalue_value' + --min_ori_evalue '$adv_param.min_ori_evalue_value' + --min_mpf_evalue '$adv_param.min_mpf_evalue' + --min_rep_ident '$adv_param.min_rep_ident' + --min_mob_ident '$adv_param.min_mob_ident' + --min_ori_ident '$adv_param.min_ori_ident' + --min_mpf_ident '$adv_param.min_mpf_ident' + --outdir '.'; + ]]> + </command> + <inputs> + <param name="input" type="data" format="zip" label="Input" help="Zipped directory of FASTA fils with contig(s)"/> + <section name="adv_param" title="Advanced parameters" expanded="False"> + <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> + <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> + <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> + <param name="min_ori_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for oriT elements blastn"/> + <param name="min_mpf_evalue" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for mpf elements blastn"/> + <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_ori_ident" label="Minimum sequence identity for oriT elements" type="integer" min="0" max="100" value="90"/> + <param name="min_mpf_ident" label="Minimum sequence identity for mpf elements" type="integer" min="0" max="100" value="80"/> + </section> + </inputs> + <outputs> + <data name="outfile1" label="${tool.name}: Plasmid report on ${input.name}" format="tabular"> + <discover_datasets pattern=".+_report\.txt" visible="true" format="tabular" assign_primary_output="true"/> + </data> + </outputs> + <tests> + <test> + <param name="input" value="plasmid_476.fasta" ftype="fasta"/> + <assert_stdout> + <has_text text="JN253636"/> + </assert_stdout> + </test> + </tests> + <help> + +**Syntax** + +This tool provides *in-silico* predictions on plasmid typing including identification of replicon, relaxase and mate-pair formation protein types. MOB-typer also predicts mobility of a plasmid (Conjugative, Mobilizable, Non-mobilizable). Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single plasmid. + +For more information please visit https://github.com/phac-nml/mob-suite/. + +----- + +**Input:** + +A FASTA file with a single or multiple contigs (e.g. plasmid.fasta): + + +**Output:** + +Tab-delimited report listing identified plasmid(s) and their predicted mobility. Refer to https://github.com/phac-nml/mob-suite#mob-typer-report-file-format for the description of each column. + + + </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>