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author | jjjjia |
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date | Tue, 28 Aug 2018 19:23:31 -0400 |
parents | 4b2738bc81ed |
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<tool id="cpo_snippy" name="CPO_Snippy" version="3.2"> <description>Modified Snippy v3.2 to support contig inputs for the cpo_prediction workflow</description> <requirements> <requirement type="package" version="3.2">snippy</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command> <![CDATA[ snippy --outdir out --cpus "\${GALAXY_SLOTS:-1}" --ref $ref $cleanup #if str( $advanced.is_advanced ) == "advanced" --mapqual $advanced.mapqual --mincov $advanced.mincov --minfrac $advanced.minfrac #if $advanced.rgid --rgid $advanced.rgid #end if #if $advanced.bwaopt --bwaopt $advanced.bwaopt #end if #end if --ctgs $input && gunzip out/snps.depth.gz && #import re #set $dir_name = ($input.element_identifier) mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ && tar -czf out.tgz ${dir_name} ]]> </command> <inputs> <param name="ref" type="data" format="fasta" label="Reference Fasta" /> <param name="input" type="data" format="fasta" label="assembled contigs"/> <param name="cleanup" type="boolean" checked="true" truevalue="--cleanup" falsevalue="" label="Cleanup the non-snp output files" help="Remove all non-SNP files: BAMs, indices etc" /> <conditional name="advanced"> <param name="is_advanced" type="select" label="Advanced parameters" help="unhide advanced parameter settings"> <option value="advanced">Show advanced settings</option> <option value="simple" selected="true">Hide advanced settings</option> </param> <when value="advanced"> <param name="mapqual" type="float" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" /> <param name="mincov" type="float" value="10" label="Minimum coverage" help="Minimum coverage to call a snp" /> <param name="minfrac" type="float" value="0.9" label="Minumum proportion for variant evidence" help="Minumum proportion for variant evidence" /> <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" /> <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" /> </when> <when value="simple"> </when> </conditional> </inputs> <outputs> <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"/> <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"/> <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"/> <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"/> <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/> <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"/> <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"/> <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"/> <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam"> <filter>cleanup is False</filter> </data> <data format="zip" name="outdir" label="${tool.name} on ${on_string} out dir" from_work_dir="out.tgz" /> </outputs> <tests> <test> <param name="ref_type_selector" value="fasta" /> <param name="ref" value="Ecoli.fna" ftype="fasta" /> <param name="fastq_input_selector" value="paired" /> <param name="fastq_input1" ftype="fastq" value="reads_1.fq" /> <param name="fastq_input2" ftype="fastq" value="reads_2.fq" /> <output name="snpsum" ftype="tabular" file="test/snps.txt" lines-diff="5" /> </test> </tests> <help> <![CDATA[ Synopsis: snippy 3.0 - fast bacterial variant calling from NGS reads Author: Torsten Seemann <torsten.seemann@gmail.com> Usage: snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz> snippy [options] --outdir <dir> --ref <ref> --se <454.fastq> snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz> Options: --help This help --version Print version and exit --citation Print citation for referencing snippy --quiet No screen output (default OFF) --cpus [N] Maximum number of CPU cores to use (default '8') --reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '') --outdir [X] Output folder (default '') --prefix [X] Prefix for output files (default 'snps') --force Force overwrite of existing output folder (default OFF) --pe1|R1|left [X] Reads, paired-end R1 (left) (default '') --pe2|R2|right [X] Reads, paired-end R2 (right) (default '') --se|single [X] Single-end reads (default '') --peil [X] Reads, paired-end R1/R2 interleaved (default '') --mapqual [n.n] Minimum mapping quality to allow (default '60') --mincov [N] Minimum coverage of variant site (default '10') --minfrac [n.n] Minumum proportion for variant evidence (default '0.9') --report Produce long report with visual alignment (slow) (default OFF) --cleanup Remove all non-SNP files: BAMs, indices etc (default OFF) --rgid [X] Use this @RG ID: in the BAM header (default '') --bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '') ]]> </help> <citations> <citation type="bibtex"> @UNPUBLISHED{Seemann2013, author = "Seemann T", title = "snippy: fast bacterial variant calling from NGS reads", year = "2015", note = "https://github.com/tseemann/snippy"} </citation> </citations> </tool>