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comparison seqtk_seq.xml @ 0:878ec9a5f8c0 draft default tip

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author matthias
date Tue, 08 Jan 2019 09:43:35 -0500
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1 <tool id="seqtk_seq" name="Convert to FASTA (seqtk)" version="0.1.0">
2 <requirements>
3 <requirement type="package" version="1.2">seqtk</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 seqtk seq
7 -a
8 $shift_quality
9 -q $quality_min
10 -X $quality_max
11 #if $mask_regions
12 -M '$maskregions'
13 #end if
14 #if $sample.sample_selector
15 -f $sample.fraction
16 #if str($sample.seed)!=''
17 -s $sample.seed
18 #end if
19 #end if
20
21 '$input1'
22 >
23 '$output1'
24 ]]></command>
25 <inputs>
26 <param type="data" name="input1" format="fastq" />
27 <param name="shift_quality" type="boolean" label="Shift quality"
28 truevalue="-V" falsevalue=""
29 help="shift quality by '(-Q) - 33' (-V)" />
30 <param name="quality_min" type="integer" label="Mask bases with quality lower than"
31 value="0" min="0" max="255" help="(-q)" />
32 <param name="quality_max" type="integer" label="Mask bases with quality higher than"
33 value="255" min="0" max="255" help="(-X)" />
34 <param name="mask_regions" type="data" label="Mask regions in BED"
35 format="bed" help="(-M)" optional="true" />
36 <conditional name="sample">
37 <param name="sample_selector" type="boolean" label="Sample fraction of sequences" />
38 <when value="true">
39 <param name="fraction" label="Fraction" type="float" value="1.0"
40 help="(-f)" />
41 <param name="seed" label="Random seed" type="integer" value=""
42 help="(-s)" optional="true" />
43 </when>
44 <when value="false">
45 </when>
46 </conditional>
47 </inputs>
48
49 <outputs>
50 <data name="output1" format="fasta" />
51 </outputs>
52 <tests>
53 <test>
54 <param name="input1" value="2.fastq"/>
55 <output name="output1" file="2.fasta"/>
56 </test>
57 <test>
58 <param name="input1" value="2.fastq"/>
59 <param name="shift_quality" value="-V"/>
60 <param name="quality_min" value="30"/>
61 <param name="quality_max" value="31"/>
62 <output name="output1" file="2.fasta"/>
63 </test>
64 </tests>
65 <help><![CDATA[
66
67 Usage: seqtk seq [options] <in.fq>|<in.fa>
68
69 Options: -q INT mask bases with quality lower than INT [0]
70 -n CHAR masked bases converted to CHAR; 0 for lowercase [0]
71 -l INT number of residues per line; 0 for 2^32-1 [0]
72 -Q INT quality shift: ASCII-INT gives base quality [33]
73 -s INT random seed (effective with -f) [11]
74 -f FLOAT sample FLOAT fraction of sequences [1]
75 -M FILE mask regions in BED or name list FILE [null]
76 -L INT drop sequences with length shorter than INT [0]
77 -c mask complement region (effective with -M)
78 -r reverse complement
79 -A force FASTA output (discard quality)
80 -C drop comments at the header lines
81
82
83 ]]></help>
84 <citations>
85 <citation type="bibtex">
86 @misc{githubseqtk,
87 author = {LastTODO, FirstTODO},
88 year = {TODO},
89 title = {seqtk},
90 publisher = {GitHub},
91 journal = {GitHub repository},
92 url = {https://github.com/lh3/seqtk},
93 }</citation>
94 </citations>
95 </tool>