staramr: staramr_search.xml comparison

comparison staramr_search.xml @ 6:3c09557ac425 draft

planemo upload for repository https://github.com/phac-nml/staramr commit 52535d98ad1e03c83c93f230abf966613b4b8fa2

author	nml
date	Tue, 30 Apr 2019 15:50:46 -0400
parents	930893c83a1a
children	f1adc47e017a

comparison

equal deleted inserted replaced

-:930893c83a1a
+:3c09557ac425
 <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>
 </requirements>
 <version_command>staramr --version</version_command>
 --nprocs "\${GALAXY_SLOTS:-1}"
 --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
 $advanced.exclude_negatives
 $advanced.exclude_resistance_phenotypes
 --exclude-genes-file '${advanced.exclude_genes.exclude_genes_file}'
 #elif str($advanced.exclude_genes.exclude_genes_condition) == 'none'
 --no-exclude-genes
 #end if
+#if str($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
 --output-excel $excel_proper_extension
 --output-hits-dir staramr_hits
-#if $use_pointfinder.enable
+#if str($use_pointfinder) != 'disabled'
---pointfinder-organism $use_pointfinder.organism
+--pointfinder-organism '${use_pointfinder}'
 #end if
 $named_genomes
 ]]></command>
 <inputs>
 <param type="data" name="genomes" format="fasta" multiple="true"/>
-<conditional name="use_pointfinder">
+<param name="use_pointfinder" type="select" label="Enable scanning for point mutations using the PointFinder database">
-<param name="enable" type="boolean" label="Enable scanning for point mutations using the PointFinder database" />
+<option value="disabled" selected="true">Disable PointFinder</option>
-<when value="true">
+<option value="salmonella">Salmonella</option>
-<param name="organism" type="select" label="Select a pointfinder organism">
+<option value="campylobacter">Campylobacter</option>
-<option value="salmonella" selected="true">Salmonella</option>
+</param>
-<option value="campylobacter">Campylobacter</option>
-</param>
-</when>
-<when value="false" />
-</conditional>
 <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)" />
 <param name="plength_resfinder" type="float" label="Percent length overlap of BLAST hit for ResFinder database" value="60.0"
 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="" />
 <param name="exclude_resistance_phenotypes" type="boolean" label="Exclude resistance phenotypes" truevalue="--exclude-resistance-phenotypes" falsevalue="" />
 <conditional name="exclude_genes">
 <when value="custom">
 <param type="data" name="exclude_genes_file" format="txt,tabular" label="Exclude genes file" help="Pass a file containing a list of genes to exclude from the ResFinder/PointFinder results" />
 </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 ${on_string}: results.xlsx" />
 <collection name="blast_hits" type="list" label="${tool.name} on ${on_string}: hits">
 <discover_datasets pattern="__name_and_ext__" directory="staramr_hits" />
 </collection>
 </outputs>
 <tests>
 <test>
 <param name="genomes" value="16S-rc_gyrA-rc_beta-lactam.fsa" />
-<conditional name="use_pointfinder">
+<param name="use_pointfinder" value="salmonella" />
-<param name="enable" value="true" />
-<param name="organism" value="salmonella" />
-</conditional>
 <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" />
 <element name="pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" file="test1-hits/pointfinder_16S-rc_gyrA-rc_beta-lactam.fsa" />
 </output_collection>
 </tests>
 <help><![CDATA[
 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
 -----
 1. Select your genome contigs (in FASTA format).
 ::
 #gene_id
 aac(6')-Iaa_1_NC_003197
+ColpVC_1__JX133088
 Output
 ------
 There are 5 different output files produced by `staramr` as well as a collection of additional files.
 summary.tsv
 ```````````
 A summary of all detected AMR genes/mutations in each genome, one genome per line.
-+------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+
++------------+-----------------------------------------------------------+-----------------------------------------------------------------------------------------------------------+-------------------------------------+
-| Isolate ID | Genotype                                                  | Predicted Phenotype                                                                                       |
+| 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 |
+| 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                                               |
+| 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
 `````````````
 A tabular file of each AMR gene and additional BLAST information from the **ResFinder** database, one gene per line.
 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
 | SRR1952926 | tet(A)     | tetracycline         | 99.92      | 100.00    | 1200/1200                | contig00027  | 1480   | 2679  | AJ517790  |
 +------------+------------+----------------------+------------+-----------+--------------------------+--------------+--------+-------+-----------+
 | 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
 ```````````````
 A tabular file of each AMR point mutation and additional BLAST information from the **PointFinder** database, one gene per line.
 The command-line, database versions, and other settings used to run `staramr`.
 ::
 command_line                  = staramr search -o out --pointfinder-organism salmonella SRR1952908.fasta SRR1952926.fasta
-version                       = 0.2.0
+version                       = 0.5.0
-start_time                    = 2018-06-05 14:41:44
+start_time                    = 2019-04-25 16:01:32
-end_time                      = 2018-06-05 14:41:47
+end_time                      = 2019-04-25 16:01:34
-total_minutes                 = 0.05
+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_commit           = e8f1eb2585cd9610c4034a54ce7fc4f93aa95535
-resfinder_db_date             = Tue, 20 Mar 2018 16:49
+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_commit         = 8706a6363bb29e47e0e398c53043b037c24b99a7
-pointfinder_db_date           = Fri, 06 Apr 2018 09:02
+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
 ``````````
 The dataset collection  **hits** stores fasta files of the specific blast hits.
 Galaxy wrapper written by Aaron Petkau at the National Microbiology Laboratory, Public Health Agency of Canada.
 .. _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>
 <citations>
 <citation type="bibtex">

Mercurial > repos > nml > staramr

comparison staramr_search.xml @ 6:3c09557ac425 draft