Mercurial > repos > thanhlv > biotradis
changeset 11:47269fae5647 draft default tip
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 4d5e56c87ec94e7853b88a4d0a6f20e411640885-dirty"
| author | thanhlv |
|---|---|
| date | Fri, 17 Jan 2020 12:47:22 -0500 |
| parents | 4e8358bc80f9 |
| children | |
| files | biotradis_bacteria_tradis.xml |
| diffstat | 1 files changed, 0 insertions(+), 20 deletions(-) [+] |
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--- a/biotradis_bacteria_tradis.xml Fri Jan 17 12:16:55 2020 -0500 +++ b/biotradis_bacteria_tradis.xml Fri Jan 17 12:47:22 2020 -0500 @@ -80,26 +80,6 @@ 3: mapping 4: creating an insertion site plot 5: creating a stats summary - - Usage: bacteria_tradis [options] - - Options: - -f : text file listing fastq files with tradis tags attached - -t : tag to search for (optional. If not set runs bwa in tagless mode with no filtering.) - -r : reference genome in fasta format (.fa) - -td : tag direction - 3 or 5 (optional. default = 3) - -mm : number of mismatches allowed when matching tag (optional. default = 0) - -m : mapping quality cutoff score (optional. default = 30) - -k : custom k-mer value (min seed length) (optional) - --smalt : use smalt rather than bwa as the mapper - --smalt_k : custom k-mer value for SMALT mapping (optional) - --smalt_s : custom step size for SMALT mapping (optional) - --smalt_y : custom y parameter for SMALT (optional. default = 0.96) - --smalt_r : custom r parameter for SMALT (optional. default = -1) - -n : number of threads to use for SMALT and samtools sort (optional. default = 1) - -e : set defaults for essentiality experiment (smalt_r = 0, -m = 0) - -v : verbose debugging output - Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_. ]]> </help> <expand macro="citations" />