Mercurial > repos > nml > staramr
diff staramr_search.xml @ 6:3c09557ac425 draft
planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2
author | nml |
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date | Tue, 30 Apr 2019 15:50:46 -0400 |
parents | 930893c83a1a |
children | f1adc47e017a |
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--- a/staramr_search.xml Tue Feb 19 16:47:25 2019 -0500 +++ b/staramr_search.xml Tue Apr 30 15:50:46 2019 -0400 @@ -1,7 +1,7 @@ <tool id="staramr_search" name="staramr" version="@VERSION@"> - <description>Scans genome assemblies against the ResFinder and PointFinder databases searching for AMR genes.</description> + <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> <macros> - <token name="@VERSION@">0.4.0</token> + <token name="@VERSION@">0.5.0</token> </macros> <requirements> <requirement type="package" version="@VERSION@">staramr</requirement> @@ -26,6 +26,7 @@ --pid-threshold $advanced.pid_threshold --percent-length-overlap-resfinder $advanced.plength_resfinder + --percent-length-overlap-plasmidfinder $advanced.plength_plasmidfinder --percent-length-overlap-pointfinder $advanced.plength_pointfinder $advanced.report_all_blast @@ -38,9 +39,15 @@ --no-exclude-genes #end if + #if str($advanced.plasmidfinder_type) != 'include_all' + --plasmidfinder-database-type '${advanced.plasmidfinder_type}' + #end if + --output-summary $summary + --output-detailed-summary $detailed_summary --output-resfinder $resfinder - #if $use_pointfinder.enable + --output-plasmidfinder $plasmidfinder + #if str($use_pointfinder) != 'disabled' --output-pointfinder $pointfinder #end if --output-settings $settings @@ -48,24 +55,19 @@ --output-hits-dir staramr_hits - #if $use_pointfinder.enable - --pointfinder-organism $use_pointfinder.organism + #if str($use_pointfinder) != 'disabled' + --pointfinder-organism '${use_pointfinder}' #end if $named_genomes ]]></command> <inputs> <param type="data" name="genomes" format="fasta" multiple="true"/> - <conditional name="use_pointfinder"> - <param name="enable" type="boolean" label="Enable scanning for point mutations using the PointFinder database" /> - <when value="true"> - <param name="organism" type="select" label="Select a pointfinder organism"> - <option value="salmonella" selected="true">Salmonella</option> - <option value="campylobacter">Campylobacter</option> - </param> - </when> - <when value="false" /> - </conditional> + <param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database"> + <option value="disabled" selected="true">Disable PointFinder</option> + <option value="salmonella">Salmonella</option> + <option value="campylobacter">Campylobacter</option> + </param> <section name="advanced" title="Advanced options" expanded="false"> <param name="pid_threshold" type="float" label="Percent identity threshold for BLAST" value="98.0" min="0" max="100" help="(--pid-threshold)" /> @@ -73,6 +75,8 @@ min="0" max="100" help="(--percent-length-overlap-resfinder)" /> <param name="plength_pointfinder" type="float" label="Percent length overlap of BLAST hit for PointFinder database" value="95.0" min="0" max="100" help="(--percent-length-overlap-pointfinder)" /> + <param name="plength_plasmidfinder" type="float" label="Percent length overlap of BLAST hit for PlasmidFinder database" value="60.0" + min="0" max="100" help="(--percent-length-overlap-plasmidfinder)" /> <param name="report_all_blast" type="boolean" label="Report all BLAST results" truevalue="--report-all-blast" falsevalue="" help="Report all BLAST results (includes overlapping hits, mainly for debugging)" /> <param name="exclude_negatives" type="boolean" label="Exclude negative (non-resistant) results" truevalue="--exclude-negatives" falsevalue="" /> @@ -89,13 +93,20 @@ </when> <when value="none" /> </conditional> + <param name="plasmidfinder_type" type="select" label="Specify PlasmidFinder Database type"> + <option value="include_all" selected="true">Include all available database types</option> + <option value="gram_positive">Gram Positive</option> + <option value="enterobacteriaceae">Enterobacteriaceae</option> + </param> </section> </inputs> <outputs> <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary.tsv" /> + <data format="tabular" name="detailed_summary" label="${tool.name} on ${on_string}: detailed_summary.tsv" /> <data format="tabular" name="resfinder" label="${tool.name} on ${on_string}: resfinder.tsv" /> + <data format="tabular" name="plasmidfinder" label="${tool.name} on ${on_string}: plasmidfinder.tsv" /> <data format="tabular" name="pointfinder" label="${tool.name} on ${on_string}: pointfinder.tsv"> - <filter>use_pointfinder['enable']</filter> + <filter>use_pointfinder != "disabled"</filter> </data> <data format="txt" name="settings" label="${tool.name} on ${on_string}: settings.txt" /> <data format="xlsx" name="excel" label="${tool.name} on ${on_string}: results.xlsx" /> @@ -106,13 +117,12 @@ <tests> <test> <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" /> - <conditional name="use_pointfinder"> - <param name="enable" value="true" /> - <param name="organism" value="salmonella" /> - </conditional> + <param name="use_pointfinder" value="salmonella" /> <output name="summary" file="test1-summary.tsv" ftype="tabular" /> + <output name="detailed_summary" file="test1-detailed-summary.tsv" ftype="tabular" /> <output name="resfinder" file="test1-resfinder.tsv" ftype="tabular" /> + <output name="plasmidfinder" file="test1-plasmidfinder.tsv" ftype="tabular" /> <output name="pointfinder" file="test1-pointfinder.tsv" ftype="tabular" /> <output_collection name="blast_hits" type="list"> <element name="resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/resfinder_16S-rc_gyrA-rc_beta-lactam.fsa" /> @@ -163,7 +173,7 @@ staramr ======= -staramr_ scans bacterial genome contigs against both the ResFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes. +staramr_ scans bacterial genome contigs against both the ResFinder_, PlasmidFinder_ and PointFinder_ databases (used by the ResFinder webservice_) and compiles a summary report of detected antimicrobial resistance genes. Usage ----- @@ -189,6 +199,7 @@ #gene_id aac(6')-Iaa_1_NC_003197 + ColpVC_1__JX133088 Output ------ @@ -200,13 +211,59 @@ A summary of all detected AMR genes/mutations in each genome, one genome per line. -+------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+ -| Isolate ID | Genotype | Predicted Phenotype | -+============+===========================================================+===========================================================================================================+ -| SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | -+------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+ -| SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | -+------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+ ++------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ +| Isolate ID | Genotype | Predicted Phenotype | Plasmid Genes | ++============+===========================================================+===========================================================================================================+=====================================+ +| SRR1952908 | aadA1, aadA2, blaTEM-57, cmlA1, gyrA (S83Y), sul3, tet(A) | streptomycin, ampicillin, chloramphenicol, ciprofloxacin I/R, nalidixic acid, sulfisoxazole, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | ++------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ +| SRR1952926 | blaTEM-57, gyrA (S83Y), tet(A) | ampicillin, ciprofloxacin I/R, nalidixic acid, tetracycline | ColpVC, IncFIB(S), IncFII(S), IncI1 | ++------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+ + +detailed_summary.tsv +```````````````````` + +A detailed summary of all detected AMR genes/mutations/plasmids in each genome, one gene per line. + ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| Isolate ID | Gene | Predicted Phenotype | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | Data Type | ++============+=============+===================================+===========+==========+=========================+=============+========+========+===========+============+ +| SRR1952908 | ColpVC | | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | Plasmid | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | Plasmid | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | IncFII(S) | | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | Plasmid | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | IncI1 | | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | Plasmid | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | aadA1 | streptomycin | 100 | 100 | 792/792 | contig00030 | 5355 | 4564 | JQ414041 | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | aadA2 | streptomycin | 100 | 100 | 780/780 | contig00030 | 7748 | 6969 | X68227 | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00032 | 6247 | 5387 | FJ405211 | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | cmlA1 | chloramphenicol | 99.92 | 100 | 1260/1260 | contig00030 | 6707 | 5448 | M64556 | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00008 | 22801 | 20165 | | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | sul3 | sulfisoxazole | 100 | 100 | 792/792 | contig00030 | 2091 | 2882 | AJ459418 | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952908 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00032 | 1476 | 2722 | AF534183 | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | ColpVC | | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | Plasmid | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | IncFIB(S) | | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | Plasmid | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | IncFII(S) | | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | Plasmid | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | IncI1 | | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | Plasmid | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | gyrA (S83Y) | ciprofloxacin I/R, nalidixic acid | 99.96 | 100 | 2637/2637 | contig00011 | 157768 | 160404 | | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ +| SRR1952926 | tet(A) | tetracycline | 99.92 | 97.8 | 1247/1275 | contig00027 | 1405 | 2651 | AF534183 | Resistance | ++------------+-------------+-----------------------------------+-----------+----------+-------------------------+-------------+--------+--------+-----------+------------+ + resfinder.tsv ````````````` @@ -233,6 +290,31 @@ | SRR1952926 | blaTEM-57 | ampicillin | 99.88 | 100.00 | 861/861 | contig00027 | 6176 | 5316 | FJ405211 | +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+ +plasmidfinder.tsv +````````````````` + +A tabular file of each AMR plasmid gene and additional BLAST information from the **PlasmidFinder** database, one plasmid gene per line. + ++------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ +| Isolate ID | Gene | %Identity | %Overlap | HSP Length/Total Length | Contig | Start | End | Accession | ++============+===========+===========+==========+=========================+=============+=======+=======+===========+ +| SRR1952908 | ColpVC | 98.96 | 100 | 193/193 | contig00038 | 1618 | 1426 | JX133088 | ++------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ +| SRR1952908 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00024 | 10302 | 9660 | FN432031 | ++------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ +| SRR1952908 | IncFII(S) | 100 | 100 | 262/262 | contig00024 | 54294 | 54555 | CP000858 | ++------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ +| SRR1952908 | IncI1 | 100 | 100 | 142/142 | contig00020 | 3907 | 3766 | AP005147 | ++------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ +| SRR1952926 | ColpVC | 98.96 | 100 | 193/193 | contig00037 | 657 | 849 | JX133088 | ++------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ +| SRR1952926 | IncFIB(S) | 98.91 | 100 | 643/643 | contig00021 | 10302 | 9660 | FN432031 | ++------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ +| SRR1952926 | IncFII(S) | 100 | 100 | 262/262 | contig00021 | 54294 | 54555 | CP000858 | ++------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ +| SRR1952926 | IncI1 | 100 | 100 | 142/142 | contig00017 | 3907 | 3766 | AP005147 | ++------------+-----------+-----------+----------+-------------------------+-------------+-------+-------+-----------+ + pointfinder.tsv ``````````````` @@ -254,25 +336,29 @@ :: command_line = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta - version = 0.2.0 - start_time = 2018-06-05 14:41:44 - end_time = 2018-06-05 14:41:47 - total_minutes = 0.05 + version = 0.5.0 + start_time = 2019-04-25 16:01:32 + end_time = 2019-04-25 16:01:34 + total_minutes = 0.04 resfinder_db_dir = staramr/databases/data/dist/resfinder resfinder_db_url = https://bitbucket.org/genomicepidemiology/resfinder_db.git - resfinder_db_commit = dc33e2f9ec2c420f99f77c5c33ae3faa79c999f2 - resfinder_db_date = Tue, 20 Mar 2018 16:49 + resfinder_db_commit = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535 + resfinder_db_date = Mon, 16 Jul 2018 16:58 pointfinder_db_dir = staramr/databases/data/dist/pointfinder pointfinder_db_url = https://bitbucket.org/genomicepidemiology/pointfinder_db.git - pointfinder_db_commit = ba65c4d175decdc841a0bef9f9be1c1589c0070a - pointfinder_db_date = Fri, 06 Apr 2018 09:02 + pointfinder_db_commit = 8706a6363bb29e47e0e398c53043b037c24b99a7 + pointfinder_db_date = Wed, 04 Jul 2018 14:27 + plasmidfinder_db_dir = staramr/databases/data/dist/plasmidfinder + plasmidfinder_db_url = https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git + plasmidfinder_db_commit = 81919954cbedaff39056610ab584ab4c06011ed8 + plasmidfinder_db_date = Tue, 20 Nov 2018 08:51 pointfinder_gene_drug_version = 050218 - resfinder_gene_drug_version = 050218 + resfinder_gene_drug_version = 050218.1 results.xlsx ```````````` -An Excel spreadsheet containing the previous 4 files as separate worksheets. +An Excel spreadsheet containing the previous 5 files as separate worksheets. BLAST Hits `````````` @@ -283,6 +369,7 @@ .. _staramr: https://github.com/phac-nml/staramr .. _ResFinder: https://bitbucket.org/genomicepidemiology/resfinder_db +.. _PlasmidFinder: https://bitbucket.org/genomicepidemiology/plasmidfinder_db .. _PointFinder: https://bitbucket.org/genomicepidemiology/pointfinder_db .. _webservice: https://cge.cbs.dtu.dk/services/ResFinder/ ]]></help>