Mercurial > repos > thanhlv > biotradis
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"
author | thanhlv |
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date | Fri, 17 Jan 2020 12:47:22 -0500 |
parents | 4e8358bc80f9 |
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10:4e8358bc80f9 | 11:47269fae5647 |
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78 1: filtering the data with tags matching that passed via -t option | 78 1: filtering the data with tags matching that passed via -t option |
79 2: removing the tags from the sequences | 79 2: removing the tags from the sequences |
80 3: mapping | 80 3: mapping |
81 4: creating an insertion site plot | 81 4: creating an insertion site plot |
82 5: creating a stats summary | 82 5: creating a stats summary |
83 | |
84 Usage: bacteria_tradis [options] | |
85 | |
86 Options: | |
87 -f : text file listing fastq files with tradis tags attached | |
88 -t : tag to search for (optional. If not set runs bwa in tagless mode with no filtering.) | |
89 -r : reference genome in fasta format (.fa) | |
90 -td : tag direction - 3 or 5 (optional. default = 3) | |
91 -mm : number of mismatches allowed when matching tag (optional. default = 0) | |
92 -m : mapping quality cutoff score (optional. default = 30) | |
93 -k : custom k-mer value (min seed length) (optional) | |
94 --smalt : use smalt rather than bwa as the mapper | |
95 --smalt_k : custom k-mer value for SMALT mapping (optional) | |
96 --smalt_s : custom step size for SMALT mapping (optional) | |
97 --smalt_y : custom y parameter for SMALT (optional. default = 0.96) | |
98 --smalt_r : custom r parameter for SMALT (optional. default = -1) | |
99 -n : number of threads to use for SMALT and samtools sort (optional. default = 1) | |
100 -e : set defaults for essentiality experiment (smalt_r = 0, -m = 0) | |
101 -v : verbose debugging output | |
102 | |
103 Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_. | 83 Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_. |
104 ]]> </help> | 84 ]]> </help> |
105 <expand macro="citations" /> | 85 <expand macro="citations" /> |
106 | 86 |
107 </tool> | 87 </tool> |