Mercurial > repos > simon-gladman > snippy
changeset 4:f0b139f53e1f draft
Added genbank support
author | simon-gladman |
---|---|
date | Tue, 07 Jun 2016 03:40:16 -0400 |
parents | 8b69e4b18a5f |
children | ff31f16f5dfd |
files | snippy.xml |
diffstat | 1 files changed, 50 insertions(+), 6 deletions(-) [+] |
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line diff
--- a/snippy.xml Mon Jun 06 00:54:10 2016 -0400 +++ b/snippy.xml Tue Jun 07 03:40:16 2016 -0400 @@ -13,11 +13,21 @@ </stdio> <command><![CDATA[ - cp $ref foo.fna && + #if str( $reftype.ref_type_selector ) == "fasta" + cp $reftype.ref foo.fna && + #end if + #if str( $reftype.ref_type_selector ) == "genbank" + cp $reftype.ref foo.gbk && + #end if snippy --outdir out --cpus "\${GALAXY_SLOTS:-1}" - --ref foo.fna + #if str( $reftype.ref_type_selector ) == "fasta" + --ref foo.fna + #end if + #if str( $reftype.ref_type_selector ) == "genbank" + --ref foo.gbk + #end if $cleanup #if str( $advanced.is_advanced ) == "advanced" --mapqual $advanced.mapqual @@ -52,7 +62,18 @@ ]]></command> <inputs> - <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" /> + <conditional name="reftype"> + <param name="ref_type_selector" type="select" label="Reference type" help="File type of the reference file. (Fasta or Genbank)"> + <option value="genbank">Genbank</option> + <option value="fasta">Fasta</option> + </param> + <when value="fasta"> + <param name="ref" type="data" format="fasta" label="Reference Fasta" help="Fasta file to use as the reference" /> + </when> + <when value="genbank"> + <param name="ref" type="data" format="genbank" label="Reference Genbank" help="Genbank file to use as the reference" /> + </when> + </conditional> <conditional name="fastq_input"> <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> <option value="paired">Paired</option> @@ -97,7 +118,7 @@ <data format="gff3" name="snpgff" label="${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 ${on_string} snps summary" from_work_dir="out/snps.txt"/> - <data format="text" name="snplog" label="${tool.name} on ${on_string} log file" from_work_dir="out/snps.log"/> + <data format="txt" name="snplog" label="${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"/> @@ -118,35 +139,58 @@ <help><![CDATA[ - This is a change to force a reinstall - Synopsis: +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>