Mercurial > repos > devteam > cd_hit_dup

comparison cd_hit_dup.xml @ 1:c8b83c5494db draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 18:52:07 -0500
parents c45a263664fd
children
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0:c45a263664fd 1:c8b83c5494db
96 <![CDATA[ 96 <![CDATA[
97 **What it does** 97 **What it does**
98 98
99 cd-hit-dup is a simple tool for removing duplicates from sequencing reads, with optional step to detect and remove chimeric reads. 99 cd-hit-dup is a simple tool for removing duplicates from sequencing reads, with optional step to detect and remove chimeric reads.
100 100
101 .. class:: infomark
102
103 **TIP:** Chimeric filtering is only available on single-ended, or joined paired-end, reads.
104
101 **Options** 105 **Options**
102 106
103 cd-hit-dup provides a number of options to tune how the duplicates are removed:: 107 cd-hit-dup provides a number of options to tune how the duplicates are removed::
104 108
105 -d Description length (default 0, truncate at the first whitespace character) 109 -d Description length (default 0, truncate at the first whitespace character)
111 its parents (default 30, minimum 20) 115 its parents (default 30, minimum 20)
112 -a Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering) 116 -a Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering)
113 -b Abundance ratio between a parent read and a chimeric read (default 1) 117 -b Abundance ratio between a parent read and a chimeric read (default 1)
114 -p Dissimilarity control for chimeric filtering (default 1) 118 -p Dissimilarity control for chimeric filtering (default 1)
115 119
116
117 ]]> 120 ]]>
118 </help> 121 </help>
119 <citations> 122 <citations>
120 <citation type="doi">10.1093/bioinformatics/bts565</citation> 123 <citation type="doi">10.1093/bioinformatics/bts565</citation>
121 </citations> 124 </citations>