Mercurial > repos > nml > ectyper
changeset 1:b02c775b27c8 draft
planemo upload for repository https://github.com/phac-nml/ecoli_serotyping commit 44fb515f2f613c2cf3c8cc17e28cd559e7555b23
| author | nml |
|---|---|
| date | Thu, 31 Jan 2019 09:39:04 -0500 |
| parents | b60c187a3a02 |
| children | e79a8dad83b4 |
| files | ectyper.xml |
| diffstat | 1 files changed, 12 insertions(+), 3 deletions(-) [+] |
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--- a/ectyper.xml Thu Jan 03 15:21:29 2019 -0500 +++ b/ectyper.xml Thu Jan 31 09:39:04 2019 -0500 @@ -19,6 +19,10 @@ ln -s "${input}" "${input.name}" && #set $genomes = $input.name #end if + + #if $mash_input + ln -s "${mash_input}" mash_sketch.msh && + #end if ectyper --cores \${GALAXY_SLOTS:-4} --input "${genomes}" @@ -27,6 +31,9 @@ #if $adv_param.verifyEcoli --verify #end if + #if $mash_input + --refseq mash_sketch.msh + #end if #if $adv_param.alleleSequence --sequence #end if @@ -34,7 +41,8 @@ ]]> </command> <inputs> - <param name="input" type="data" format="fastq,fasta" label="Input(s)" help="FASTA or FASTQ file(s) with contig(s)"/> + <param name="input" type="data" format="fastq,fasta" label="Genome(s) input(s)" help="FASTA or FASTQ file(s) with contig(s)"/> + <param name="mash_input" type="data" optional="true" format="binary" label="Mash genome sketches (Optional)" help="Optionally provide MASH sketches to find closest genome (in case O/H typing fails)"/> <section name="adv_param" title="Advanced parameters" expanded="False"> <param name="min_percentIdentity" type="integer" value="90" min="1" max="100"/> <param name="percentLength" type="integer" value="50" min="1" max="100"/> @@ -75,8 +83,9 @@ **Input:** -Accepts a variety of inputs including single or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results draft assemblies are recommended. +Accepts a variety of inputs including single or multiple FASTQ and/or FASTA file(s). Inputs might contain pure raw reads, but for more accurate results draft assemblies are recommended. +Optionally select a MASH RefSeq genome sketch (version 2.0 and above) for cases when O/H typing would fail. Download RefSeq genome sketch containing 91,283 genomes with 1000 hashes each directly from https://gembox.cbcb.umd.edu/mash/refseq.genomes.k21s1000.msh . **Output:** @@ -101,4 +110,4 @@ url = {https://github.com/phac-nml/ecoli_serotyping} }</citation> </citations> -</tool> +</tool> \ No newline at end of file