Mercurial > repos > card > rgi
diff rgi.xml @ 0:715bc9aeef69 draft
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188
| author | card |
|---|---|
| date | Wed, 27 Feb 2019 09:08:21 -0500 |
| parents | |
| children | f96cbb663aa9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgi.xml Wed Feb 27 09:08:21 2019 -0500 @@ -0,0 +1,187 @@ +<tool id="rgi" name="Resistance Gene Identifier (RGI)" version="4.2.2"> + <description>This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models.</description> + <requirements> + <requirement type="package" version="4.2.2">rgi</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ +#if $db_opts.db_opts_selector != "default": + rgi load + #if $db_opts.db_opts_selector == "local": + -i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json" + #else: + -i "$db_opts.rgi_db_hist" + #end if + --local + && +#end if + +rgi main + -i '$input_sequence' + -o out + -t $input_type + -a $alignment_tool + -n "\${GALAXY_SLOTS:-1}" + $include_loose + $low_quality + -d $data + +#if $db_opts.db_opts_selector != "default": + --local +#end if + ]]></command> + <inputs> + <param argument="--input_sequence" type="data" format="fastq,fasta" label="Input sequence" help="input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz"/> + <param argument="--input_type" type="select" multiple="false" label="Input type" help="specify data input type (default = contig)"> + <option value="contig" selected="true">CONTIG (Nucleotide Sequence)</option> + <option value="protein">PROTEIN (Protein Sequence)</option> + </param> + <param argument="--alignment_tool" type="select" label="Alignment tool" help="specify alignment tool (default = BLAST)"> + <option value="blast" selected="true">BLAST</option> + <option value="diamond">DIAMOND</option> + </param> + <param argument="--include_loose" type="boolean" checked="false" truevalue="--include_loose" falsevalue="" label="Include loose hits" help="include loose hits in addition to strict and perfect hits"/> + <param argument="--low_quality" type="boolean" checked="false" truevalue="--low_quality" falsevalue="" label="Low quality" help="use for short contigs to predict partial genes"/> + <param argument="--data" type="select" multiple="false" label="Data type" help="specify a data-type (default = NA)"> + <option value="wgs">WGS</option> + <option value="plasmid">PLASMID</option> + <option value="chromosome">CHROMOSOME</option> + <option value="NA" selected="true">NA</option> + </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Select an RGI database"> + <option value="default" selected="true">Default RGI database</option> + <option value="local">Locally installed RGI database</option> + <option value="hist">RGI database from your history</option> + </param> + <when value="default"> + <param name="rgi_db_local" type="hidden" value="" /> + <param name="rgi_db_hist" type="hidden" value="" /> + </when> + <when value="local"> + <param name="rgi_db_local" type="select" multiple="false" label="Locally installed RGI database"> + <options from_data_table="rgi_databases"> + <validator type="no_options" message="No databases are available built-in"/> + </options> + </param> + <param name="rgi_db_hist" type="hidden" value="" /> + </when> + <when value="hist"> + <param name="rgi_db_local" type="hidden" value="" /> + <param name="rgi_db_hist" type="data" format="json" label="RGI database from your history" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="report" format="json" from_work_dir="out.json" label="${tool.name} on ${on_string}: report.json"/> + <data name="summary" format="tabular" from_work_dir="out.txt" label="${tool.name} on ${on_string}: summary.txt"/> + </outputs> + <tests> + <test> + <param name="input_sequence" value="test1.fasta" /> + <param name="input_type" value="contig" /> + <param name="alignment_tool" value="blast" /> + <param name="include_loose" value="false" /> + <param name="low_quality" value="false" /> + <param name="data" value="NA" /> + <conditional name="db_opts"> + <param name="db_opts_selector" value="default" /> + </conditional> + <output name="summary"> + <assert_contents> + <has_text text="AY123251" /> + </assert_contents> + </output> + </test> + </tests> + <help> + <![CDATA[ +Resistance Gene Identifier (RGI) +================================ + +RGI is used to predict resistome(s) from protein or nucleotide data based on homology and SNP models. The tool uses data from the CARD database. + +Usage +----- + +1. Select your input sequence (in FASTA format). +2. Select your input type (CONTIG or PROTEIN). +3. Select your alignment tool (DIAMOND or BLAST). +4. Specify if you want to include loose hits (YES or NO). +5. Specify if you want to remove temporary files (YES or NO). +6. Specify if you want to low quality predictions (YES or NO). +7. Select your data type (WGS, PLASMID, CHROMOSOME or NA). +8. Run the tool. + +Output +------ + +There are 2 different output files produced by `rgi`. + +summary.txt +^^^^^^^^^^^ + +A tabular file of all detected resistance genes, one gene per line. + ++--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+ +| ORF_ID | Contig | Start | Stop | Orientation | Cut_Off | Pass_Bitscore | Best_Hit_Bitscore | Best_Hit_ARO | Best_Identities | ARO | Model_type | SNPs_in_Best_Hit_ARO | Other_SNPs | Drug Class | Resistance Mechanism | AMR Gene Family | Predicted_DNA | Predicted_Protein | CARD_Protein_Sequence | Percentage Length of Reference Sequence | ID | Model_ID | ++==========================================================================================================================+===============+=======+======+=============+==========+================+=====================+================+==================+==========+=======================+==========================+=============+============+=========================+======================+===========================+========================+===========================+=========================================+================================+===========+ +| AY123251.1_6 # 3575 # 4489 # 1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399 | AY123251.1_6 | 3575 | 4489 | \+ | Strict | 500 | 506.908 | CARB-7 | 83.68 | 3002246 | protein homolog model | n/a | n/a | penam | antibiotic inactivation | CARB beta-lactamase | ATGC | MLLYKMCDNQNYGVTYMKFLLV | MKSLLVFALLMPSVVFASSSKFQSV | 105.56 | gnl|BL_ORD_ID|589|hsp_num:0 | 1443 | ++--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+ + +report.json +^^^^^^^^^^^ + +A json version of summary.txt. + +Help +---- + +**usage:** + ``rgi main [-h] -i INPUT_SEQUENCE -o OUTPUT_FILE [-t {read,contig,protein,wgs}] [-a {DIAMOND,BLAST}] [-n THREADS] [--include_loose] [--local] [--clean] [--debug] [--low_quality] [-d {wgs,plasmid,chromosome,NA}] [-v]`` + +**optional arguments:** + +- ``-h, --help`` + show this help message and exit +- ``-i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE`` + input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz +- ``-o OUTPUT_FILE, --output_file OUTPUT_FILE`` + output folder and base filename +- ``-t {read,contig,protein,wgs}, --input_type {read,contig,protein,wgs}`` + specify data input type (default = contig) +- ``-a {DIAMOND,BLAST}, --alignment_tool {DIAMOND,BLAST}`` + specify alignment tool (default = BLAST) +- ``-n THREADS, --num_threads THREADS`` + number of threads (CPUs) to use in the BLAST search (default=8) +- ``--include_loose`` + include loose hits in addition to strict and perfect hits +- ``--local`` + use local database (default: uses database in executable directory) +- ``--clean`` + removes temporary files +- ``--debug`` + debug mode +- ``--low_quality`` + use for short contigs to predict partial genes +- ``-d {wgs,plasmid,chromosome,NA}, --data {wgs,plasmid,chromosome,NA}`` + specify a data-type (default = NA) +- ``-v, --version`` + prints software version number + +Links +----- + +RGI: https://card.mcmaster.ca/analyze/rgi + +Github: https://github.com/arpcard/rgi + +CARD database: https://card.mcmaster.ca + ]]> + </help> + <citations> + <citation type="doi">10.1093/nar/gkw1004</citation> + </citations> +</tool>