Mercurial > repos > rnateam > atactk_trim_adapters

annotate trim_adapters.xml @ 0:3d64d2a625a1 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
author rnateam
date Wed, 20 Jun 2018 15:47:23 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
1 <tool id="atactk_trim_adapters" name="Trim putative adapter sequence" version="0.1.6">
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
2 <requirements>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
3 <requirement type="package" version="0.1.6">atactk</requirement>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
4 </requirements>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
5 <command detect_errors="exit_code"><![CDATA[
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
6 ln -s '$input1' ./forward.${input1.ext} &&
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
7 ln -s '$input2' ./reverse.${input2.ext} &&
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
8 trim_adapters
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
9 #if '$settings.advanced' == 'advanced'
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
10 -d '$settings.edit_distance'
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
11 -f '$settings.fudge'
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
12 -s '$settings.trim_start'
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
13 -r '$settings.rc_length'
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
14 #end if
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
15 ./forward.${input1.ext} ./reverse.${input2.ext}
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
16 ]]></command>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
17 <inputs>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
18 <param type="data" name="input1" format="fastq,fastq.gz" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
19 <param type="data" name="input2" format="fastq,fastq.gz" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
20 <conditional name="settings">
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
21 <param name="advanced" type="select" label="Specify advanced parameters">
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
22 <option value="simple" selected="true">No, use program defaults.</option>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
23 <option value="advanced">Yes, see full parameter list.</option>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
24 </param>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
25 <when value="simple"></when>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
26 <when value="advanced">
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
27 <param name="edit_distance" label="The maximum edit distance permitted when aligning the paired reads" type="integer" min="1" value="1" help="(-d)" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
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)" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
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)"/>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
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)"/>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
31 </when>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
32 </conditional>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
33 </inputs>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
34 <outputs>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
35 <data name="output1" format="fastq.gz" from_work_dir="forward.trimmed.fastq.gz" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
36 <data name="output2" format="fastq.gz" from_work_dir="reverse.trimmed.fastq.gz" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
37 </outputs>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
38 <tests>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
39 <test>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
40 <param name="input1" value="SP1_f.fastq" ftype="fastq" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
41 <param name="input2" value="SP1_r.fastq" ftype="fastq" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
42 <output name="output1" file="SP1_f.trimmed.fastq.gz" decompress="True"/>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
43 <output name="output2" file="SP1_r.trimmed.fastq.gz" decompress="True"/>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
44 </test>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
45 <test>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
46 <param name="input1" value="SP1_f.fastq.gz" ftype="fastq.gz" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
47 <param name="input2" value="SP1_r.fastq.gz" ftype="fastq.gz" />
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
48 <output name="output1" file="SP1_f.trimmed.fastq.gz" decompress="True"/>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
49 <output name="output2" file="SP1_r.trimmed.fastq.gz" decompress="True"/>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
50 </test>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
51 </tests>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
52 <help>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
53 <![CDATA[
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
54
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
55 **What it does**
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
56
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
57 The trim_adapters utility is based on a script by Jason Buenrostro.
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
58 Instead of looking for known adapter sequence, it aligns paired reads to each other
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
59 and trims off sequence outside the alignment. More precisely, it searches
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
60 the forward read for the reverse complement of a specified number of bases
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
61 (20 by default) at the beginning of the reverse read, then falls back to finding
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
62 the best alignment of the two reads, using the minimum Levenshtein distance between them.
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
63
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
64 **Input**
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
65
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
66 It requires 2 inputs: The (optionally gzipped) FASTQ file containing the
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
67 forward reads and the (optionally gzipped) FASTQ file containing the
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
68 reverse reads.
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
69
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
70 **Output**
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
71
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
72 Generates 2 gzipped fastq files with adapters trimmed.
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
73
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
74 ]]></help>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
75 <citations>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
76 <citation type="bibtex">@unpublished{atactk: a toolkit for ATAC-seq data,
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
77 title = "atactk: a toolkit for ATAC-seq data",
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
78 author = "The Parker Lab at the University of Michigan",
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
79 url = "https://github.com/ParkerLab/atactk/",
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
80 year = "2018"
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
81 }</citation>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
82 </citations>
3d64d2a625a1 planemo upload for repository https://github.com/bgruening/galaxytools/blob/master/tools/trim_adapters commit 3d0b670cda6522e5c442b144785b2f9f517f103d
rnateam
parents:
diff changeset
83 </tool>