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planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
author rnateam
date Wed, 20 Jun 2018 15:48:09 -0400
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1 <tool id="atactk_trim_adapters" name="Trim putative adapter sequence" version="0.1.6">
2 <requirements>
3 <requirement type="package" version="0.1.6">atactk</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 ln -s '$input1' ./forward.${input1.ext} &&
7 ln -s '$input2' ./reverse.${input2.ext} &&
8 trim_adapters
9 #if '$settings.advanced' == 'advanced'
10 -d '$settings.edit_distance'
11 -f '$settings.fudge'
12 -s '$settings.trim_start'
13 -r '$settings.rc_length'
14 #end if
15 ./forward.${input1.ext} ./reverse.${input2.ext}
16 ]]></command>
17 <inputs>
18 <param type="data" name="input1" format="fastq,fastq.gz" />
19 <param type="data" name="input2" format="fastq,fastq.gz" />
20 <conditional name="settings">
21 <param name="advanced" type="select" label="Specify advanced parameters">
22 <option value="simple" selected="true">No, use program defaults.</option>
23 <option value="advanced">Yes, see full parameter list.</option>
24 </param>
25 <when value="simple"></when>
26 <when value="advanced">
27 <param name="edit_distance" label="The maximum edit distance permitted when aligning the paired reads" type="integer" min="1" value="1" help="(-d)" />
28 <param name="fudge" label="An arbitrary number of extra bases to trim from the ends of reads" type="integer" min="1" value="1" help="(-f)" />
29 <param name="trim_start" label="Trim this number of bases from the start of each sequence" type="integer" min="0" value="0" help="(-s)"/>
30 <param name="rc_length" label="Use the reverse complement of this number of from the beginning of the reverse read to align reads" type="integer" min="1" value="20" help="(-r)"/>
31 </when>
32 </conditional>
33 </inputs>
34 <outputs>
35 <data name="output1" format="fastq.gz" from_work_dir="forward.trimmed.fastq.gz" />
36 <data name="output2" format="fastq.gz" from_work_dir="reverse.trimmed.fastq.gz" />
37 </outputs>
38 <tests>
39 <test>
40 <param name="input1" value="SP1_f.fastq" ftype="fastq" />
41 <param name="input2" value="SP1_r.fastq" ftype="fastq" />
42 <output name="output1" file="SP1_f.trimmed.fastq.gz" decompress="True"/>
43 <output name="output2" file="SP1_r.trimmed.fastq.gz" decompress="True"/>
44 </test>
45 <test>
46 <param name="input1" value="SP1_f.fastq.gz" ftype="fastq.gz" />
47 <param name="input2" value="SP1_r.fastq.gz" ftype="fastq.gz" />
48 <output name="output1" file="SP1_f.trimmed.fastq.gz" decompress="True"/>
49 <output name="output2" file="SP1_r.trimmed.fastq.gz" decompress="True"/>
50 </test>
51 </tests>
52 <help>
53 <![CDATA[
54
55 **What it does**
56
57 The trim_adapters utility is based on a script by Jason Buenrostro.
58 Instead of looking for known adapter sequence, it aligns paired reads to each other
59 and trims off sequence outside the alignment. More precisely, it searches
60 the forward read for the reverse complement of a specified number of bases
61 (20 by default) at the beginning of the reverse read, then falls back to finding
62 the best alignment of the two reads, using the minimum Levenshtein distance between them.
63
64 **Input**
65
66 It requires 2 inputs: The (optionally gzipped) FASTQ file containing the
67 forward reads and the (optionally gzipped) FASTQ file containing the
68 reverse reads.
69
70 **Output**
71
72 Generates 2 gzipped fastq files with adapters trimmed.
73
74 ]]></help>
75 <citations>
76 <citation type="bibtex">@unpublished{atactk: a toolkit for ATAC-seq data,
77 title = "atactk: a toolkit for ATAC-seq data",
78 author = "The Parker Lab at the University of Michigan",
79 url = "https://github.com/ParkerLab/atactk/",
80 year = "2018"
81 }</citation>
82 </citations>
83 </tool>