Mercurial > repos > jowong > snippy_mod
changeset 0:55e3a2bbcde6 draft default tip
planemo upload
| author | jowong |
|---|---|
| date | Mon, 29 Oct 2018 11:24:34 -0400 |
| parents | |
| children | |
| files | macros.xml snippy.xml |
| diffstat | 2 files changed, 204 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 29 11:24:34 2018 -0400 @@ -0,0 +1,25 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">snippy</requirement> + <yield /> + </requirements> + </xml> + + <xml name="version_command"> + <version_command><![CDATA[snippy --version]]></version_command> + </xml> + + <token name="@VERSION@">3.2</token> + + <xml name="citations"> + <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@UNPUBLISHED{Seemann2013, + author = "Seemann T", + title = "snippy: fast bacterial variant calling from NGS reads", + year = "2015", + note =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", + url = "https://github.com/tseemann/snippy"}</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snippy.xml Mon Oct 29 11:24:34 2018 -0400 @@ -0,0 +1,179 @@ +<tool id="snippy_mod" name="snippy_mod" version="@VERSION@"> + <description> + Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + + <command detect_errors="exit_code"><![CDATA[ + + #if $ref.is_of_type("fasta") + cp '$ref' 'foo.fna' && + #end if + #if $ref.is_of_type("genbank") + cp '$ref' 'foo.gbk' && + #end if + snippy + --outdir 'out' + --cpus "\${GALAXY_SLOTS:-1}" + #if $ref.is_of_type("fasta") + --ref 'foo.fna' + #end if + #if $ref.is_of_type("genbank") + --ref 'foo.gbk' + #end if + --mapqual $adv.mapqual + --mincov $adv.mincov + --minfrac $adv.minfrac + #if $adv.rgid + --rgid '$advanced.rgid' + #end if + #if $adv.bwaopt + --bwaopt '$advanced.bwaopt' + #end if + + #if str( $fastq_input.fastq_input_selector ) == "paired" + --pe1 '$fastq_input.fastq_input1' + --pe2 '$fastq_input.fastq_input2' + #end if + #if str( $fastq_input.fastq_input_selector ) == "paired_collection" + --pe1 '$fastq_input.fastq_input1.forward' + --pe2 '$fastq_input.fastq_input1.reverse' + #end if + #if str( $fastq_input.fastq_input_selector ) == "single" + --se '$fastq_input.fastq_input1' + #end if + #if str( $fastq_input.fastq_input_selector ) == "paired_iv" + --peil '$fastq_input.fastq_input1' + #end if + + + ]]></command> + + <inputs> + + <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" /> + + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> + <option value="paired">Paired</option> + <option value="single">Single</option> + <option value="paired_collection">Paired Collection</option> + <option value="paired_iv">Paired Interleaved</option> + </param> + <when value="paired"> + <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> + <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> + </when> + <when value="single"> + <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/> + </when> + <when value="paired_collection"> + <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> + </when> + <when value="paired_iv"> + <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> + </when> + </conditional> + + <section name="adv" title="Advanced parameters" expanded="false"> + <param name="mapqual" type="integer" value="60" label="Minimum mapping quality" help="Minimum mapping quality to allow" /> + <param name="mincov" type="integer" 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" /> + </section> + + <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection"> + <option value="outvcf" selected="True">The final annotated variants in VCF format</option> + <option value="outgff" selected="False">The variants in GFF3 format</option> + <option value="outtab" selected="True">A simple tab-separated summary of all the variants</option> + <option value="outsum" selected="False">A summary of the samples and mapping</option> + <option value="outlog" selected="False">A log file with the commands run and their outputs</option> + <option value="outaln" selected="False">A version of the reference but with - at position with depth=0 and N for 0 to depth to --mincov (does not have variants)</option> + <option value="outcon" selected="False">A version of the reference genome with all variants instantiated</option> + <option value="outdep" selected="False">Output of samtools depth for the .bam file</option> + <option value="outbam" selected="False">The alignments in BAM format. Note that multi-mapping and unmapped reads are not present.</option> + </param> + + </inputs> + + <outputs> + + <data format="vcf" name="snpvcf" label="${tool.name} on ${on_string} snps vcf file" from_work_dir="out/snps.vcf"> + <filter>outputs and 'outvcf' in outputs</filter> + </data> + <data format="gff3" name="snpgff" label="${tool.name} on ${on_string} snps gff file" from_work_dir="out/snps.gff"> + <filter>outputs and 'outgff' in outputs</filter> + </data> + <data format="tabular" name="snptab" label="${tool.name} on ${on_string} snps table" from_work_dir="out/snps.tab"> + <filter>outputs and 'outtab' in outputs</filter> + </data> + <data format="tabular" name="snpsum" label="${tool.name} on ${on_string} snps summary" from_work_dir="out/snps.txt"> + <filter>outputs and 'outsum' in outputs</filter> + </data> + <data format="txt" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"> + <filter>outputs and 'outlog' in outputs</filter> + </data> + <data format="fasta" name="snpalign" label="${tool.name} on ${on_string} aligned fasta" from_work_dir="out/snps.aligned.fa"> + <filter>outputs and 'outaln' in outputs</filter> + </data> + <data format="fasta" name="snpconsensus" label="${tool.name} on ${on_string} consensus fasta" from_work_dir="out/snps.consensus.fa"> + <filter>outputs and 'outcon' in outputs</filter> + </data> + <data format="tabular" name="snpsdepth" label="${tool.name} on ${on_string} mapping depth" from_work_dir="out/snps.depth"> + <filter>outputs and 'outdep' in outputs</filter> + </data> + <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam"> + <filter>outputs and 'outbam' in outputs</filter> + </data> + + </outputs> + + <tests> + + + + </tests> + + + <help><![CDATA[ + +**Snippy @VERSION@** + + Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). + +**Author** + + Torsten Seemann + +**Inputs** + + - NGS Reads in fastq format (single or paired end) + - Reference file in either fasta or genbank format + +If the reference file is supplied in genbank format, snpeff will be called to determine the effect of any snps found. + +**Advanced options** + + - mapping quality - Integer - Minimum mapping quality to allow (default '60') + + - minimum coverage - Integer - Minimum coverage of variant site (default '10') + + - minimum fraction - Float - Minumum proportion for variant evidence (default '0.9') + + - rgid - String - Use this @RG ID: in the BAM header (default '') + + - bwaopt - Extra BWA MEM options, eg. -x pacbio (default '') + +**Further information** + + For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy + + ]]></help> + <expand macro="citations"/> + +</tool>