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