comparison biotradis_bacteria_tradis.xml @ 11:47269fae5647 draft default tip

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 4d5e56c87ec94e7853b88a4d0a6f20e411640885-dirty"

10:4e8358bc80f9

        1: filtering the data with tags matching that passed via -t option
        2: removing the tags from the sequences
        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>
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</tool>

11:47269fae5647

        1: filtering the data with tags matching that passed via -t option
        2: removing the tags from the sequences
        3: mapping
        4: creating an insertion site plot
        5: creating a stats summary
        Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_.
    ]]>    </help>
    <expand macro="citations" />

</tool>