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annotate ucsb_phylogenetics/trimmingreads/TrimmingReads.xml @ 4:5b23f3eb3f09 draft

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Added sequence gap remover and Trimming Reads.
author ucsb-phylogenetics
date Sun, 24 Jun 2012 16:02:29 -0400
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children eb55013e0f28
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1 <tool id="trimming_reads" name="TrimmingReads">
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2 <description>Runs TrimmingReads</description>
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3 <command interpreter="perl">TrimmingReads.pl -i $input -l $l_int -o out.fastq -r $r_int -q $q_int -n $len_int</command>
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4 <inputs>
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5 <param name="input" label="Input file" type="data" format="fastq"/>
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6 <param name="l_int" label="Left Trim Bases" type="integer" value="0" />
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7 <param name="r_int" label="Right Trim Bases" type="integer" value="0" />
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8 <param name="q_int" label="Qual Cut Off" type="integer" value="0"/>
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9 <param name="len_int" label="Length Cut Off" type="integer" value="0"/>
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10 </inputs>
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11 <outputs>
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12 <data from_work_dir="out.fastq" format="fastq" />
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13 </outputs>
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14
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15 <help>
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16
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17 Trimming Reads is a part of the NGS QC Toolkit.
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18
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19 This tool trims the reads/sequences and their quality scores (in case of FASTQ file) in two ways.
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20 First, it trims fixed (user-specified) number of bases from 5’ and/or 3’ end of the reads and corresponding qualities from the input FASTQ file.
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21 Second, it trims low quality bases from 3’ end of the read using user-defined threshold value of quality score.
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22 Input to this tool is either FASTQ or FASTA format file.
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23 Options are provided to specify the number of bases to be trimmed and the quality threshold for quality based trimming.
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24 (http://59.163.192.90:8080/ngsqctoolkit/NGSQCToolkitv2.2.3_manual.pdf)
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25
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26 http://59.163.192.90:8080/ngsqctoolkit/
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27
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28 http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030619
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29 Patel RK, Jain M (2012). NGS QC Toolkit: A toolkit for quality control of next generation sequencing data. PLoS ONE, 7(2): e30619.
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30
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31 Left Trim
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32 </help>
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33 </tool>