Mercurial > repos > estrain > srst2v2
changeset 1:d381880c66f1 draft default tip
Deleted selected files
| author | estrain |
|---|---|
| date | Tue, 28 Nov 2017 22:35:03 -0500 |
| parents | 0869a76e692b |
| children | |
| files | srst2_fda.xml |
| diffstat | 1 files changed, 0 insertions(+), 173 deletions(-) [+] |
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--- a/srst2_fda.xml Tue Nov 28 22:34:44 2017 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,173 +0,0 @@ -<tool id="srst2" name="SRST2 - Short Read Sequence Typer (v2)" version="0.2.0"> - <requirements> - <requirement type="package" version="0.2.0">srst2</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - #if $paired_conditional.sPaired == "paired" - ln -s $paired_conditional.fastq1 sample_1.fastq; - ln -s $paired_conditional.fastq2 sample_2.fastq; - #end if - - srst2 - - #if $paired_conditional.sPaired == "single" - --input_se $paired_conditional.fastq1 - #else if $paired_conditional.sPaired == "paired" - --input_pe sample_1.fastq sample_2.fastq - #end if - - --output srst2out - --save_scores - --mlst_definitions "$mlst_definitions" - --mlst_db "$mlst_db" - --mlst_delimiter $mlstdelim - --mlst_max_mismatch $mlst_max_mismatch - - ]]></command> - <inputs> - <conditional name="paired_conditional"> - <param name="sPaired" type="select" label="Single-End or Paired-End FASTQ?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - </param> - <when value="single"> - <param name="fastq1" type="data" format="fastq" label="FASTQ file" help="FASTQ" /> - </when> - <when value="paired"> - <param name="fastq1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ" /> - <param name="fastq2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ" /> - </when> - </conditional> - - <param type="data" name="mlst_db" label="Fasta file of MLST alleles" format="fasta" /> - <param type="data" name="mlst_definitions" label="ST definitions for MLST scheme" format="tabular" /> - <param type="text" name="mlstdelim" value="_" format="txt" label="Character(s) separating gene name from allele number in MLST database (default '_')" /> - <param type="integer" name="mlst_max_mismatch" value="10" format="txt" label="Maximum number of mismatches per read for MLST allele calling (default 10)" /> - </inputs> - - <outputs> - <data format="txt" label="Scores" name="scores" from_work_dir="*.scores"/> - <data format="bam" label="bam alignment" name="bam" from_work_dir="*.sorted.bam"/> - <data format="pileup" label="pileup" name="pileup" from_work_dir="*.pileup"/> - <data format="txt" label="Alleles" name="alleles" from_work_dir="*results.txt"/> - </outputs> - - <help><![CDATA[ - -SRST2 - Short Read Sequence Typer (v2) - -This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. - - - -optional arguments: - -h, --help show this help message and exit - --version show program's version number and exit - --input_se INPUT_SE - Single end read file(s) for analysing (may be gzipped) - --input_pe INPUT_PE - Paired end read files for analysing (may be gzipped) - --merge_paired Switch on if all the input read sets belong to a - single sample, and you want to merge their data to get - a single result - --forward FORWARD Designator for forward reads (only used if NOT in - MiSeq format sample_S1_L001_R1_001.fastq.gz; otherwise - default is _1, i.e. expect forward reads as - sample_1.fastq.gz) - --reverse REVERSE Designator for reverse reads (only used if NOT in - MiSeq format sample_S1_L001_R2_001.fastq.gz; otherwise - default is _2, i.e. expect forward reads as - sample_2.fastq.gz - --read_type READ_TYPE - Read file type (for bowtie2; default is q=fastq; other - options: qseq=solexa, f=fasta). - --mlst_db MLST_DB Fasta file of MLST alleles (optional) - --mlst_delimiter MLST_DELIMITER - Character(s) separating gene name from allele number - in MLST database (default "-", as in arcc-1) - --mlst_definitions MLST_DEFINITIONS - ST definitions for MLST scheme (required if mlst_db - supplied and you want to calculate STs) - --mlst_max_mismatch MLST_MAX_MISMATCH - Maximum number of mismatches per read for MLST allele - calling (default 10) - --gene_db GENE_DB - Fasta file/s for gene databases (optional) - --no_gene_details Switch OFF verbose reporting of gene typing - --gene_max_mismatch GENE_MAX_MISMATCH - Maximum number of mismatches per read for gene - detection and allele calling (default 10) - --min_coverage MIN_COVERAGE - Minimum %coverage cutoff for gene reporting (default - 90) - --max_divergence MAX_DIVERGENCE - Maximum %divergence cutoff for gene reporting (default - 10) - --min_depth MIN_DEPTH - Minimum mean depth to flag as dubious allele call - (default 5) - --min_edge_depth MIN_EDGE_DEPTH - Minimum edge depth to flag as dubious allele call - (default 2) - --prob_err PROB_ERR Probability of sequencing error (default 0.01) - --truncation_score_tolerance TRUNCATION_SCORE_TOLERANCE - % increase in score allowed to choose non-truncated - allele - --stop_after STOP_AFTER - Stop mapping after this number of reads have been - mapped (otherwise map all) - --other OTHER - Other arguments to pass to bowtie2 (must be escaped, - e.g. "\\--no-mixed".) - --max_unaligned_overlap MAX_UNALIGNED_OVERLAP - Read discarded from alignment if either of its ends - has unaligned overlap with the reference that is - longer than this value (default 10) - --mapq MAPQ Samtools -q parameter (default 1) - --baseq BASEQ Samtools -Q parameter (default 20) - --samtools_args SAMTOOLS_ARGS - Other arguments to pass to samtools mpileup (must be - escaped, e.g. "\\-A"). - --output OUTPUT Prefix for srst2 output files - --log Switch ON logging to file (otherwise log to stdout) - --save_scores Switch ON verbose reporting of all scores - --report_new_consensus - If a matching alleles is not found, report the - consensus allele. Note, only SNP differences are - considered, not indels. - --report_all_consensus - Report the consensus allele for the most likely - allele. Note, only SNP differences are considered, not - indels. - --use_existing_bowtie2_sam - Use existing SAM file generated by Bowtie2 if - available, otherwise they will be generated - --use_existing_pileup - Use existing pileups if available, otherwise they will - be generated - --use_existing_scores - Use existing scores files if available, otherwise they - will be generated - --keep_interim_alignment - Keep interim files (sam & unsorted bam), otherwise - they will be deleted after sorted bam is created - --threads THREADS Use multiple threads in Bowtie and Samtools - --prev_output PREV_OUTPUT - SRST2 results files to compile (any new results from - this run will also be incorporated) - - - ]]></help> - - - <citations> - <citation type="bibtex"> - @misc{pope_dashnow_zobel_holt_raven_schultz_inouye_tomita_2014, - title={SRST2: Rapid genomic surveillance for public health and hospital microbiology labs}, - url={https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-014-0090-6}, - journal={Genome Medicine}, publisher={BioMed Central}, - author={Pope, Bernard J and Dashnow, Harriet and Zobel, Justin and Holt, Kathryn E and Raven, Lesley-Ann and Schultz, Mark B and Inouye, Michael and Tomita, Takehiro}, - year={2014}, month={Nov}} , - }</citation> - </citations> -</tool>