Mercurial > repos > artbio > yac_clipper

comparison yac.xml @ 7:396bc2c718a1 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit a30e10dfaf7ba8a1b6e38075f058b11186790c74
author artbio
date Tue, 29 Nov 2022 08:58:44 +0000
parents acbf910cd2ae
children
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6:acbf910cd2ae 7:396bc2c718a1
1 <tool id="yac" name="Clip adapter" version="2.5.0"> 1 <tool id="yac" name="Clip adapter" version="2.5.1">
2 <description /> 2 <description />
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.7.6">python</requirement> 4 <requirement type="package" version="3.7.6">python</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
147 + Filters sequences on their size 147 + Filters sequences on their size
148 + Filters sequences containing unknown nucleotides (optional) 148 + Filters sequences containing unknown nucleotides (optional)
149 149
150 ------- 150 -------
151 151
152 yac_clipper clips 7nt long motives in 5' of adapter sequences. 152 yac_clipper clips 7nt long motives in 5' of adapter sequences. *It is accepting 1 mismatch in the searched 7nt motif.*
153
154 It also accepts 1 mismatch in the searched 7nt motif
155 153
156 **Inputs** 154 **Inputs**
157 155
158 1. A fastq or fasta file of reads to be clipped 156 1. A fastq or fasta file of reads to be clipped
159 2. Select the size of the reads to be kept 157 2. Select the size of the reads to be kept
160 3. Select an output format. When input is a fastq file, this may be fastq or fasta, whereas 158 3. Select an output format. When input is a fastq file, this may be fastq or fasta, whereas
161 when input is a fasta file, this only may be a fasta. 159 when input is a fasta file, this only may be a fasta.
162 4. Select whether you wish or do not wish to keep clipped sequences with unknown nucleotides (N) 160 4. Select whether you wish or do not wish to keep clipped sequences with unknown nucleotides (N)
163 5. Select a pre-built adapter sequence or enter your own sequence (at least 7 nucleotides long) 161 5. Select a pre-built adapter sequence or enter your own sequence (at least 7 nucleotides long)
164 162
165 ------- 163 -------
166 164