|
0
|
1 <tool id="seqtk_seq" name="Convert to FASTA (seqtk)" version="0.1.0">
|
|
|
2 <requirements>
|
|
|
3 <requirement type="package" version="1.0-r68">seqtk</requirement>
|
|
|
4 </requirements>
|
|
|
5 <stdio>
|
|
|
6 <exit_code range="1:" />
|
|
|
7 </stdio>
|
|
|
8 <command><![CDATA[
|
|
|
9 seqtk seq
|
|
|
10 $shift_quality
|
|
|
11 -q $quality_min
|
|
|
12 -X $quality_max
|
|
|
13 -a "$input1" > "$output1"
|
|
|
14 ]]></command>
|
|
|
15 <inputs>
|
|
|
16 <param type="data" name="input1" format="fastq" />
|
|
|
17 <param name="shift_quality" type="boolean" label="Shift quality"
|
|
|
18 truevalue="-V" falsevalue=""
|
|
|
19 help="shift quality by '(-Q) - 33' (-V)" />
|
|
|
20 <param name="quality_min" type="integer" label="Mask bases with quality lower than"
|
|
|
21 value="0" min="0" max="255" help="(-q)" />
|
|
|
22 <param name="quality_max" type="integer" label="Mask bases with quality higher than"
|
|
|
23 value="255" min="0" max="255" help="(-X)" />
|
|
|
24 </inputs>
|
|
|
25 <outputs>
|
|
|
26 <data name="output1" format="fasta" />
|
|
|
27 </outputs>
|
|
|
28 <tests>
|
|
|
29 <test>
|
|
|
30 <param name="input1" value="2.fastq"/>
|
|
|
31 <output name="output1" file="2.fasta"/>
|
|
|
32 </test>
|
|
|
33 </tests>
|
|
|
34 <help><![CDATA[
|
|
|
35
|
|
|
36 Usage: seqtk seq [options] <in.fq>|<in.fa>
|
|
|
37
|
|
|
38 Options: -q INT mask bases with quality lower than INT [0]
|
|
|
39 -X INT mask bases with quality higher than INT [255]
|
|
|
40 -n CHAR masked bases converted to CHAR; 0 for lowercase [0]
|
|
|
41 -l INT number of residues per line; 0 for 2^32-1 [0]
|
|
|
42 -Q INT quality shift: ASCII-INT gives base quality [33]
|
|
|
43 -s INT random seed (effective with -f) [11]
|
|
|
44 -f FLOAT sample FLOAT fraction of sequences [1]
|
|
|
45 -M FILE mask regions in BED or name list FILE [null]
|
|
|
46 -L INT drop sequences with length shorter than INT [0]
|
|
|
47 -c mask complement region (effective with -M)
|
|
|
48 -r reverse complement
|
|
|
49 -A force FASTA output (discard quality)
|
|
|
50 -C drop comments at the header lines
|
|
|
51 -N drop sequences containing ambiguous bases
|
|
|
52 -1 output the 2n-1 reads only
|
|
|
53 -2 output the 2n reads only
|
|
|
54 -V shift quality by '(-Q) - 33'
|
|
|
55 -U convert all bases to uppercases
|
|
|
56
|
|
|
57
|
|
|
58 ]]></help>
|
|
|
59 <citations>
|
|
|
60 <citation type="bibtex">
|
|
|
61 @misc{githubseqtk,
|
|
|
62 author = {LastTODO, FirstTODO},
|
|
|
63 year = {TODO},
|
|
|
64 title = {seqtk},
|
|
|
65 publisher = {GitHub},
|
|
|
66 journal = {GitHub repository},
|
|
|
67 url = {https://github.com/lh3/seqtk},
|
|
|
68 }</citation>
|
|
|
69 </citations>
|
|
|
70 </tool> |
