Mercurial > repos > estrain > amrfinderplus_db
changeset 0:ca2967a24e27 draft
Uploaded
| author | estrain |
|---|---|
| date | Tue, 24 May 2022 01:08:44 +0000 |
| parents | |
| children | 80909e07d176 |
| files | amrfinderplus_db/amrfinderplus.loc.sample amrfinderplus_db/amrfinderplus_db.xml amrfinderplus_db/tool-data/amrfinderplus.loc amrfinderplus_db/tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 149 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/amrfinderplus_db/amrfinderplus.loc.sample Tue May 24 01:08:44 2022 +0000 @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of amrfinder databases +# +# the columns are: +# value name path +# +# for example +# 2021-04-14 May22DB /tmp/tool-data/amrfinderdatabases/May22DB
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/amrfinderplus_db/amrfinderplus_db.xml Tue May 24 01:08:44 2022 +0000 @@ -0,0 +1,128 @@ +<tool id="amrfinderplus_db" name="amrfinderplus_db" version="@VERSION@+galaxy1"> + <description> + NCBI AMRFinderPlus tool - utilizes Data Manager (data_manager_amrfinderplus) + </description> + <macros> + <token name="@VERSION@">3.10.23</token> + </macros> + <requirements> + <requirement type="package" version="@VERSION@">ncbi-amrfinderplus</requirement> + </requirements> + <version_command><![CDATA[amrfinder --version]]></version_command> + + <command detect_errors="exit_code"><![CDATA[ + amrfinder + $plus + --threads \${GALAXY_SLOTS:-1} + --database '$amrfinder_databases.fields.path' + #if $input_selection.input_source_selector == 'nuc' + -n '$input_selection.fasta_file' + #elif $input_selection.input_source_selector == 'pro' + -p '$input_selection.fasta_file' + #if $input_selection.gff.use == 'gff_yes' + -g '$input_selection.gff.gff_file' + #end if + #elif $input_selection.input_source_selector == 'both' + -n '$input_selection.nuc_file' + -p '$input_selection.pro_file' + #if $input_selection.gff.use == 'gff_yes' + -g '$input_selection.gff.gff_file' + #end if + #end if + #if str($organism) != 'None' + -O $organism + #end if + -o results.tsv + $report_common + #if $mutation_all == "true" + --mutation_all mutation_all.tsv + #end if + $gpipe + ]]> </command> + + <inputs> + <conditional name="input_selection"> + <param name="input_source_selector" type="select" label="Input data type"> + <option value="nuc">Nucleotide</option> + <option value="pro">Protein</option> + <option value="both">Nucleotide and Protein</option> + </param> + <when value="nuc"> + <param name="fasta_file" type="data" format="fasta" label="Select nucleotide fasta file"/> + </when> + <when value="pro"> + <param name="fasta_file" type="data" format="fasta" label="Select protein fasta file"/> + <conditional name="gff"> + <param name="use" type="select" label="Using GFF to get genomic coordinates"> + <option value="gff_yes">Yes</option> + <option value="gff_no" selected="true">No</option> + </param> + <when value="gff_yes"> + <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/> + </when> + <when value="gff_no"> + </when> + </conditional> + </when> + <when value="both"> + <param name="nuc_file" type="data" format="fasta" label="Select a nucleotide fasta file"/> + <param name="pro_file" type="data" format="fasta" label="Select a protein fasta file"/> + <conditional name="gff"> + <param name="use" type="select" label="Using GFF to get genomic coordinates"> + <option value="gff_yes">Yes</option> + <option value="gff_no" selected="true">No</option> + </param> + <when value="gff_yes"> + <param name="gff_file" type="data" format="gff,gff3" label="Select GFF file" help="Protein id should be in the attribute 'Name=id' (9th field) of the rows with type 'CDS' or 'gene' (3rd field)."/> + </when> + <when value="gff_no"> + </when> + </conditional> + </when> + </conditional> + <!-- DATABASE INPUT--> + <param name="amrfinder_databases" label="Select a database" type="select"> + <options from_data_table="amrfinderplus"> + <validator message="No database is available" type="no_options" /> + </options> + </param> + <param name="organism" type="select" optional="true" label="Get organism-specific results"> + <option value="Campylobacter">Campylobacter</option> + <option value="Escherichia">Escherichia</option> + <option value="Klebsiella">Klebsiella</option> + <option value="Salmonella">Salmonella</option> + <option value="Staphylococcus">Staphylococcus</option> + <option value="Vibrio">Vibrio</option> + </param> + <param name="min_iden" argument="--ident_min" type="float" value="-1" label="Minimum identity for a blast-based hit" help="(Methods BLAST or PARTIAL). -1 means use a curated threshold if it exists and 0.9 otherwise. Setting this value to something other than -1 will override any curated similarity cutoffs" /> + <param name="min_cov" argument="--coverage_min" type="float" min="0" max="1" value="0.5" label="Minimum coverage of the reference protein" /> + <param name="plus" type="boolean" truevalue="--plus" falsevalue="" label="Add the plus genes to the report" /> + <param name="report_common" type="boolean" truevalue="--report_common" falsevalue="" label="Suppress proteins common to a taxonomy group" /> + <param name="mutation_all" type="boolean" truevalue="true" falsevalue="false" label="Report all target positions of mutations" /> + <param name="gpipe" type="boolean" truevalue="--gpipe" falsevalue="" label="Protein identifiers in the protein FASTA file have format gnl-project-accession" /> + </inputs> + + <outputs> + <data name="result" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Result"/> + <data name="all_mutations" format="tabular" from_work_dir="mutation_all.tsv" label="${tool.name} on ${on_string}: All Mutations"> + <filter>mutation_all</filter> + </data> + </outputs> + + <tests> + </tests> + + + <help><![CDATA[ + This software and the accompanying database are designed to find acquired + antimicrobial resistance genes in bacterial protein or assembled nucleotide + sequences as well as known point mutations for several taxa. With + AMRFinderPlus we have added select members of additional classes of genes + such as virulence factors, biocide, heat, acid, and metal resistance genes. + More details: https://github.com/ncbi/amr/wiki + ]]> </help> + <citations> + <citation type="doi">10.1101/550707</citation> + </citations> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/amrfinderplus_db/tool-data/amrfinderplus.loc Tue May 24 01:08:44 2022 +0000 @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of amrfinder databases +# +# the columns are: +# value name path +# +# for example +# 2021-04-14 May22DB /tmp/tool-data/amrfinderdatabases/May22DB
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/amrfinderplus_db/tool_data_table_conf.xml.sample Tue May 24 01:08:44 2022 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of amrfinderplus database in the required format --> + <table name="amrfinderplus" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, path</columns> + <file path="tool-data/amrfinderplus.loc" /> + </table> +</tables>