diff 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"

--- 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" />