| Previous changeset 9:93ba63eaf394 (2021-08-05) Next changeset 11:179497074102 (2025-02-26) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob-suite commit 8bd2d0ff4101e7e7e6a45247d616929593a03cd4 |
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modified:
macros.xml mob_recon.xml mob_typer.xml |
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| diff -r 93ba63eaf394 -r 2fd93022d5d7 macros.xml --- a/macros.xml Thu Aug 05 21:53:36 2021 +0000 +++ b/macros.xml Fri Feb 21 18:41:14 2025 +0000 |
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| @@ -1,5 +1,10 @@ <macros> - <token name="@VERSION@">3.0.3</token> + <token name="@VERSION@">3.1.9</token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">mob_suite</xref> + </xrefs> + </xml> <xml name="requirements"> <requirements> <requirement type="package" version ="@VERSION@">mob_suite</requirement> |
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| diff -r 93ba63eaf394 -r 2fd93022d5d7 mob_recon.xml --- a/mob_recon.xml Thu Aug 05 21:53:36 2021 +0000 +++ b/mob_recon.xml Fri Feb 21 18:41:14 2025 +0000 |
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| b'@@ -2,7 +2,8 @@\n <description>Type contigs and extract plasmid sequences</description>\n <macros>\n <import>macros.xml</import>\n- </macros> \n+ </macros> \n+ <expand macro="bio_tools"/> \n <expand macro="requirements" />\n <version_command>mob_recon --version</version_command>\n <command detect_errors="exit_code">\n@@ -14,7 +15,7 @@\n ln -s \'$input\' \'$named_input\' &&\n \n \n- mob_recon --num_threads \\${GALAXY_SLOTS:-4} --infile \'${named_input}\' --run_typer\n+ mob_recon --num_threads \\${GALAXY_SLOTS:-4} --infile \'${named_input}\'\n \n #if $adv_param.unicycler_contigs:\n --unicycler_contigs \n@@ -56,6 +57,16 @@\n --plasmid_orit \'$adv_param.plasmid_orit\'\n #end if\n \n+ #if $adv_param.filter_db\n+ --filter_db \'$adv_param.filter_db\'\n+ #end if\n+\n+ --mash_genome_neighbor_threshold \'${adv_param.mash_genome_neighbor_threshold}\'\n+ --primary_cluster_dist \'${adv_param.primary_cluster_dist}\'\n+ --secondary_cluster_dist \'${adv_param.secondary_cluster_dist}\'\n+ --max_contig_size \'${adv_param.max_contig_size}\'\n+ --max_plasmid_size \'${adv_param.max_plasmid_size}\'\n+\n --min_length \'${adv_param.min_length}\' \n --min_rep_evalue \'${adv_param.min_rep_evalue}\'\n --min_rep_evalue \'${adv_param.min_rep_evalue}\'\n@@ -70,6 +81,8 @@\n --min_mob_cov \'${adv_param.min_mob_cov}\'\n --min_con_cov \'${adv_param.min_con_cov}\'\n --min_rpp_cov \'${adv_param.min_rpp_cov}\'\n+ \n+ \n --outdir \'outdir\' &&\n mkdir ./outdir/plasmids && (mv outdir/plasmid*.fasta ./outdir/plasmids 2> /dev/null || true)\n ]]> \n@@ -77,40 +90,50 @@\n <inputs>\n <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>\n <section name="adv_param" title="Advanced parameters" expanded="False">\n- <param name="unicycler_contigs" type="boolean" truevalue="true" falsevalue="" checked="true" label="Check for circularity flag generated by unicycler in contigs fasta headers?"/>\n- <param name="run_overhang" type="boolean" truevalue="true" falsevalue="" checked="true" label="Detect circular contigs (i.e. potential plasmids) with assembly overhangs?"/> \n- <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?"/>\n+ \n+ <param name="unicycler_contigs" type="boolean" truevalue="true" falsevalue="" checked="true" label="Check for circularity flag generated by unicycler in contigs fasta headers?" help="(--unicycler_contigs)"/>\n+ <param name="run_overhang" type="boolean" truevalue="true" falsevalue="" checked="true" label="Detect circular contigs (i.e. potential plasmids) with assembly overhangs?" help="(--run_overhang)"/> \n+ <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" help="(--debug)"/>\n+ <param name="mash_genome_neighbor_threshold" label="Mash distance selecting valid closed genomes to filter" type="float" min="0.00001" max="1" value="0.002" help="(--mash_genome_neighbor_threshold)"/>\n+ <param name="primary_cluster_dist" label="MASH distance for assigning primary plasmid cluster id" type="float" min="0.00001" max="1" value="0.06" help="(--primary_cluster_dist)"/>\n+ <param name="secondary_cluster_dist" label="MASH distance for assigning secondary plasmid cluster id" type="float" min="0.00001" max="1" value="0.025" help="(--secondary_cluster_dist)"/>\n+ <param name="max_contig_size" label="Maximum size of a contig to be considered a plasmid (bp)" type="integer" min="1" max="1000000" value="450000" help="(--max_contig_size)"/> \n+ <param name="max_plasmid_size" label="Maximum size of a reconstructed plasmid (bp)" type="integer" min="1" max="1000000" value="450000" help="(--max_plasmid_size)"/> \n \n- <param name="min_rep_evalue" label="Minimum evalue threshold for replicon blastn" type="float" min="0.00001" max="1" value="0.00001"/>\n- <param name="min_mob_evalue" label="Minimum eval'..b'optional="true" format="fasta" label="FASTA of plasmid relaxases" help=""/>\n- <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help=""/>\n- <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help=""/>\n+ <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference custom database of complete plasmids" help="(--plasmid_db)"/>\n+ <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="MASH sketch of the reference plasmids database (--plasmid_mash_db)"/>\n+ <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="(--plasmid_meta)"/>\n+ <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="(--plasmid_replicons)"/>\n+ <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="(--reptitive_mask)"/>\n+ <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="(--plasmid_mob)"/>\n+ <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="(--plasmid_mpf)"/>\n+ <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="(--plasmid_orit)"/>\n+ <param name="filter_db" type="data" optional="true" format="fasta" label="Path to fasta file to mask sequences" help="(--filter_db)"/>\n+\n+ \n+ \n </section> \n </inputs>\n <outputs>\n <data name="contig_report" format="tabular" from_work_dir="outdir/contig_report.txt" label="${tool.name} on ${input.element_identifier}: Overall contig MOB-recon report"/> \n <data name="mobtyper_aggregate_report" format="tabular" from_work_dir="outdir/mobtyper_results.txt" label="${tool.name} on ${input.element_identifier}: Aggregate MOB-typer report for all contigs"/>\n- <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: Chromosomal sequences"/>\n- <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: Plasmids">\n+ <data name="chromosome" format="fasta" from_work_dir="outdir/chromosome.fasta" label="${tool.name} on ${input.element_identifier}: CHROMOSOMAL contigs"/>\n+ <collection name="plasmids" type="list" label="${tool.name} on ${input.element_identifier}: PLASMIDS RECONSTRUCTED">\n <discover_datasets pattern="__name_and_ext__" directory="outdir/plasmids" />\n </collection>\n </outputs>\n@@ -146,10 +169,6 @@\n \n For more information please visit https://github.com/phac-nml/mob-suite/. \n \n-**Workflow**\n-\n-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.\n-\n -----\n \n **Input:**\n@@ -161,7 +180,7 @@\n \n 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.\n \n-Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.\n+**Note:** Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.\n \n \n </help>\n' |
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| diff -r 93ba63eaf394 -r 2fd93022d5d7 mob_typer.xml --- a/mob_typer.xml Thu Aug 05 21:53:36 2021 +0000 +++ b/mob_typer.xml Fri Feb 21 18:41:14 2025 +0000 |
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| b'@@ -3,6 +3,7 @@\n <macros>\n <import>macros.xml</import>\n </macros>\n+ <expand macro="bio_tools"/>\n <expand macro="requirements"/>\n <version_command>mob_typer --version</version_command>\n <command detect_errors="exit_code">\n@@ -60,6 +61,11 @@\n #if $adv_param.debug\n --debug\n #end if\n+ \n+ #if $adv_param.biomarker_report_file\n+ --biomarker_report_file biomarker_report.txt\n+ #end if\n+ \n \n --out_file plasmid_report.txt;\n \n@@ -68,31 +74,34 @@\n <inputs>\n <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>\n <section name="adv_param" title="Advanced parameters" expanded="False">\n- <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independant plasmid?" />\n- <param name="min_rep_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for replicon blastn"/> \n- <param name="min_mob_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for relaxase tblastn"/> \n- <param name="min_con_evalue_value" type="float" value="0.00001" min="0.00001" max="1" label="Minimum evalue threshold for contig blastn"/> \n- <param name="min_length" type="integer" value="1000" label="Minimum length of contigs to classify"/> \n- <param name="min_rep_ident" label="Minimum sequence identity for replicons" type="integer" min="0" max="100" value="80"/>\n- <param name="min_mob_ident" label="Minimum sequence identity for relaxases" type="integer" min="0" max="100" value="80"/>\n- <param name="min_con_ident" label="Minimum sequence identity for contigs" type="integer" min="0" max="100" value="80"/>\n- <param name="min_rep_cov" label="Minimum percentage coverage of replicon query by input assembly" type="integer" min="0" max="100" value="80"/>\n- <param name="min_mob_cov" label="Minimum percentage coverage of relaxase query by input assembly" type="integer" min="0" max="100" value="80"/>\n- <param name="min_con_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="integer" min="0" max="100" value="70"/>\n- <param name="min_overlap" label="Minimum overlap of fragments" type="integer" min="0" max="100" value="10"/>\n- <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" />\n- <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help=""/>\n- <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="Companion MASH database of reference database"/>\n- <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="MOB-cluster plasmid cluster formatted metadata file matched to the reference plasmid db"/>\n- <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="FASTA of plasmid replicons"/>\n- <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="FASTA of known repetitive elements"/>\n- <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="FASTA of plasmid relaxases"/>\n- <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="FASTA of known plasmid mate-pair proteins"/>\n- <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT dna sequences"/>\n+ <param name="multi" type="boolean" truevalue="true" falsevalue="" checked="false" label="Treat each input sequence as an independent plasmid?" help'..b'"80" help="(--min_mob_cov)"/>\n+ <param name="min_con_cov" label="Minimum percentage coverage of assembly contig by the plasmid reference database to be considered" type="integer" min="0" max="100" value="70" help="(--min_con_cov)"/>\n+ <param name="min_overlap" label="Minimum overlap of fragments (bp)" type="integer" min="0" max="100" value="10" help="(--min_overlap)"/>\n+ <param name="debug" type="boolean" truevalue="true" falsevalue="" checked="false" label="Provide debug information?" help="(--debug)"/>\n+ <param name="plasmid_db" optional="true" type="data" format="fasta" label="Reference Database of complete plasmids" help="(--plasmid_db)"/>\n+ <param name="plasmid_mash_db" optional="true" type="data" format="binary" label="Custom MASH database of plasmids" help="Custom MASH plasmid reference database (--plasmid_mash_db)"/>\n+ <param name="plasmid_meta" type="data" optional="true" format="text" label="Plasmid cluster metadata file" help="MOB-cluster plasmid cluster formatted metadata file matched to the reference plasmid database (--plasmid_meta)"/>\n+ <param name="plasmid_replicons" type="data" optional="true" format="fasta" label="FASTA file with plasmid replicons" help="FASTA of plasmid replicons custom database (--plasmid_replicons)"/>\n+ <param name="repetitive_mask" type="data" optional="true" format="fasta" label="FASTA of known repetitive elements" help="FASTA of known repetitive elements custom database (--repetitive_mask)"/>\n+ <param name="plasmid_mob" type="data" optional="true" format="fasta" label="FASTA of plasmid relaxases" help="FASTA of plasmid relaxases custom database (--plasmid_mob)"/>\n+ <param name="plasmid_mpf" type="data" optional="true" format="fasta" label="FASTA of known plasmid mate-pair proteins" help="FASTA of known plasmid mate-pair proteins custom database (--plasmid_mpf)"/>\n+ <param name="plasmid_orit" type="data" optional="true" format="fasta" label="FASTA of known plasmid oriT dna sequences" help="FASTA of known plasmid oriT DNA sequences custom database (--plasmid_orit)"/>\n </section>\n </inputs>\n <outputs>\n <data name="plasmid_report" from_work_dir="plasmid_report.txt" label="${tool.name}: Plasmid report on ${input.element_identifier}" format="tabular" />\n+ <data name="biomarker_report" from_work_dir="biomarker_report.txt" label="${tool.name}: Biomarker report on ${input.element_identifier}" format="tabular" />\n </outputs>\n <tests>\n <test>\n@@ -114,7 +123,7 @@\n \n **Syntax**\n \n-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.\n+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) and potential host range. \n \n For more information please visit https://github.com/phac-nml/mob-suite/. \n \n@@ -127,9 +136,9 @@\n \n **Output:**\n \n-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.\n+Tab-delimited report listing identified plasmid(s) and their predicted mobility and host range and optionally a biomarker report (if selected). Refer to https://github.com/phac-nml/mob-suite#mob-typer-report-file-format for the description of each column.\n \n-\n+**Note:** Do not include multiple unrelated plasmids in the input FASTA file as they will be treated as a single plasmid or turn on the **--multi** parameter (i.e. *Treat each input sequence as an independent plasmid?*).\n </help>\n <citations>\n <citation type="bibtex">\n' |