# HG changeset patch # User dfornika # Date 1573692420 0 # Node ID bcf6aa9dbc77a13a13a8172ab31fda5b604ca142 # Parent cd69d25ce45124819eca398bc9e3ed6e5fa0f663 "planemo upload for repository https://github.com/phac-nml/mob-suite commit d5db17429118cd74a85986c49b917caec6f952bd-dirty" diff -r cd69d25ce451 -r bcf6aa9dbc77 1.4/mob_recon.xml --- a/1.4/mob_recon.xml Thu Nov 14 00:43:21 2019 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,127 +0,0 @@ - - Type contigs and extract plasmid sequences - - mob_suite - - - /dev/null || true) - ]]> - - - -
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- - -**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. - - - - - - @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} - } - -
diff -r cd69d25ce451 -r bcf6aa9dbc77 1.4/mob_typer.xml --- a/1.4/mob_typer.xml Thu Nov 14 00:43:21 2019 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,81 +0,0 @@ - - Get the plasmid type and mobility given its sequence - - mob_suite - - - - - - -
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- - - - - - - - - - - - - - - -**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. - - - - - - @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} - } - -