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comparison trimming3.xml @ 2:621da360a155 draft

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author czlab
date Thu, 17 May 2018 21:33:10 -0400
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1 <tool id="trimming3" name="Trim 3' adapter">
2 <description> using FASTX Toolkit</description>
3
4 <command>
5 fastx_clipper -a $adapterSeq -l $discardShorterThan $discardNonclipped $discardClipped $adapterOnly $keepUnknown
6 #if $minAdapterAlignment.minOverlapRequired =="yes":
7 -M $minAdapterAlignment.minLen
8 #end if
9 -v -i $input 2>/dev/null | fastq_quality_trimmer -v -l $discardShorterThan -t $qualityThreshold -o $output
10 </command>
11
12 <inputs>
13 <param name="input" type="data" format="fastq" label="Input FASTQ file"/>
14
15 <param name="adapterSeq" type="text" value="" label="Adapter sequence (the 3' adapter will vary for different CLIP protocol variations)"/>
16 <param name="discardShorterThan" type="integer" value="" label="Discard sequences shorter than N nucleotides (see help below for parameter suggestion)"/>
17 <param name="discardNonclipped" type="boolean" truevalue="-c" falsevalue="" checked="no" label="Discard non-trimmed sequences (i.e. - keep only sequences which contained the adapter)" />
18 <param name="discardClipped" type="boolean" truevalue="-C" falsevalue="" checked="no" label="Discard trimmed sequences (i.e. - keep only sequences which did not contained the adapter)" />
19 <param name="adapterOnly" type="boolean" truevalue="-k" falsevalue="" checked="no" label="Report Adapter-Only sequences"/>
20 <param name="keepUnknown" type="boolean" truevalue="-n" falsevalue="" checked="yes" label="Keep sequences with unknown nucleotides"/>
21 <conditional name="minAdapterAlignment">
22 <param name="minOverlapRequired" type="select" label="Require minimum adapter alignment length of N. If less than N nucleotides aligned with the adapter - don't trim it.">
23 <option value="yes">Yes</option>
24 <option value="no" selected="True">No</option>
25 </param>
26 <when value="yes">
27 <param name="minLen" type="integer" value="" label="Input the length"/>
28 </when>
29 <when value="no">
30 </when>
31 </conditional>
32 <param name="qualityThreshold" type="integer" value="5" label="Quality threshold - nucleotides with lower quality will be trimmed (from the end of the sequence)"/>
33 <!--<param name="CompressOutput" type="boolean" truevalue="-z" falsevalue="" checked="no" label="Compress output with GZIP"/> -->
34
35 </inputs>
36
37 <outputs>
38 <data name="output" format="fastq" label="Trim 3' adapter on ${on_string} "/>
39 </outputs>
40 <help>
41
42 .. class:: infomark
43
44 **What this tool does**
45
46
47 This tool takes as input FASTQ files and output FASTQ files with 3' adapters and extremely low quality bases (e.g. score less than 5) removed.
48
49 It is a wrapper of fastx_clipper and fastq_quality_trimmer that are a part of the FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
50
51 -----
52
53 **Parameter suggestion for discarding sequences**
54
55 We typically require high quality score in barcode and 15 nt of CLIP tags.
56 * For standard CLIP: discard sequences shorter than 20 nt (5 nt barcode + 15 nt CLIP tag).
57 * For BrdU CLIP: discard sequences shorter than 29 nucleotides (14 nt barcode + 15 nt CLIP tag).
58
59 </help>
60
61 </tool>