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planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Tue, 21 Jul 2015 14:14:43 -0400
parents 2e150ed1b76e
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0:2e150ed1b76e 1:0fb894bd8eba
1 <tool id="cd_hit_dup" name="cd-hit-dup" version="0.0.1"> 1 <tool id="cd_hit_dup" name="cd-hit-dup" version="0.0.1">
2 <description>
3 remove duplicates and detect chimaeras in sequencing reads
4 </description>
2 <requirements> 5 <requirements>
3 <requirement type="package" version="0.5-2012-03-07-fix-dan-gh-0.0.1">cd-hit-auxtools</requirement> 6 <requirement type="package" version="0.5-2012-03-07-fix-dan-gh-0.0.1">cd-hit-auxtools</requirement>
4 </requirements> 7 </requirements>
5 <stdio> 8 <stdio>
6 <exit_code range="1:" /> 9 <exit_code range="1:" />
41 <when value="paired"> 44 <when value="paired">
42 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/> 45 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
43 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/> 46 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
44 </when> 47 </when>
45 <when value="single"> 48 <when value="single">
46 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select read dataset" help="Specify dataset with single reads"/> 49 <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select reads" help="Specify dataset with single reads"/>
47 <conditional name="filter_chimeras"> 50 <conditional name="filter_chimeras">
48 <param name="filter_chimeras_selector" type="select" label="Filter out chimeric clusters"> 51 <param name="filter_chimeras_selector" type="select" label="Filter out chimeric clusters">
49 <option value="true">Yes</option> 52 <option value="true">Yes</option>
50 <option value="false" selected="True">No</option> 53 <option value="false" selected="True">No</option>
51 </param> 54 </param>
89 <output name="output_chimeric_clusters" ftype="tabular" file="cd-hit-dup_out_chimera.chimeric_clusters.tabular" /> 92 <output name="output_chimeric_clusters" ftype="tabular" file="cd-hit-dup_out_chimera.chimeric_clusters.tabular" />
90 </test> 93 </test>
91 </tests> 94 </tests>
92 <help> 95 <help>
93 <![CDATA[ 96 <![CDATA[
94 **What it does** 97 **What it does**
95 98
96 cd-hit-dup is a simple tool for removing duplicates from sequencing reads, with optional step to detect and remove chimeric reads. A number of options are provided to tune how the duplicates are removed. 99 cd-hit-dup is a simple tool for removing duplicates from sequencing reads, with optional step to detect and remove chimeric reads.
97 100
101 **Options**
98 102
99 **Options** 103 cd-hit-dup provides a number of options to tune how the duplicates are removed::
100 104
101 +--------+-------------------------------------------------------------------------------------------------------------------+ 105 -d Description length (default 0, truncate at the first whitespace character)
102 | Option | Description | 106 -u Length of prefix to be used in the analysis (default 0, for full/maximum length)
103 +========+===================================================================================================================+ 107 -m Match length (true/false, default true)
104 |-i | Input file | 108 -e Maximum number/percent of mismatches allowed
105 +--------+-------------------------------------------------------------------------------------------------------------------+ 109 -f Filter out chimeric clusters (true/false, default false)
106 |-i2 | Second input file | 110 -s Minimum length of common sequence shared between a chimeric read and each of
107 +--------+-------------------------------------------------------------------------------------------------------------------+ 111 its parents (default 30, minimum 20)
108 |-o | Output file | 112 -a Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering)
109 +--------+-------------------------------------------------------------------------------------------------------------------+ 113 -b Abundance ratio between a parent read and a chimeric read (default 1)
110 |-d | Description length (default 0, truncate at the first whitespace character) | 114 -p Dissimilarity control for chimeric filtering (default 1)
111 +--------+-------------------------------------------------------------------------------------------------------------------+
112 |-u | Length of prefix to be used in the analysis (default 0, for full/maximum length) |
113 +--------+-------------------------------------------------------------------------------------------------------------------+
114 |-m | Match length (true/false, default true) |
115 +--------+-------------------------------------------------------------------------------------------------------------------+
116 |-e | Maximum number/percent of mismatches allowed |
117 +--------+-------------------------------------------------------------------------------------------------------------------+
118 |-f | Filter out chimeric clusters (true/false, default false) |
119 +--------+-------------------------------------------------------------------------------------------------------------------+
120 |-s | Minimum length of common sequence shared between a chimeric read and each of its parents (default 30, minimum 20) |
121 +--------+-------------------------------------------------------------------------------------------------------------------+
122 |-a | Abundance cutoff (default 1 without chimeric filtering, 2 with chimeric filtering) |
123 +--------+-------------------------------------------------------------------------------------------------------------------+
124 |-b | Abundance ratio between a parent read and a chimeric read (default 1) |
125 +--------+-------------------------------------------------------------------------------------------------------------------+
126 |-p | Dissimilarity control for chimeric filtering (default 1) |
127 +--------+-------------------------------------------------------------------------------------------------------------------+
128 115
129 116
130 ]]> 117 ]]>
131 </help> 118 </help>
132 <citations> 119 <citations>