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annotate lighter.xml @ 0:89b453176d05 draft

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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
author bgruening
date Sat, 04 Jun 2016 12:38:34 -0400
parents
children b0cfd92907eb
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0
89b453176d05 planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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1 <tool id="lighter" name="lighter" version="1.0" profile="16.04">
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2 <description>can correct the reads containing sequence errors</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.1">lighter</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 lighter
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8 #for $file in $r:
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9 -r $file
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10 #end for
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11 #if str($kmer.k_select) == "smallk":
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12 -k $kmer.k_parameter_string
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13 #elif str($kmer.k_select) == "bigK":
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14 -K $kmer.K_parameter_string
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15 #end if
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16 -od ./
89b453176d05 planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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17 -t \${GALAXY_SLOTS:-4}
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18 #if $maxcor:
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19 -maxcor $maxcor
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20 #end if
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21 $trim
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22 $discard
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23 $noQual
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24 #if $newQual:
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25 -newQual '$newQual'
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26 #end if
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27 $stable
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28 > $outfile
89b453176d05 planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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29 ]]>
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30 </command>
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31 <inputs>
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32 <param argument="-r" multiple="True" type="data" label="Input file"/>
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33 <conditional name="kmer">
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34 <param name="k_select" type="select" label="Do you want k or K?">
89b453176d05 planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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35 <option value="smallk">small k</option>
89b453176d05 planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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36 <option value="bigK">big K</option>
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37 </param>
89b453176d05 planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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38 <when value="smallk">
89b453176d05 planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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39 <param name="k_parameter_string" size="30" type="text" value="13 20 0.2" label="type in 3 parameters"
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40 help="(—k kmer_length genome_size alpha)" />
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41 </when>
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42 <when value="bigK">
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43 <param name="K_parameter_string" size="30" type="text" value="13 20" label="type in 2 parameters"
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44 help="(—K kmer_length genome_size)" />
89b453176d05 planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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45 </when>
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46 </conditional>
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47 <param argument="-maxcor" type="integer" value="4" optional="True"
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48 label="Maximum number of correction for within a kmer length window" help=""/>
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49 <param argument="-trim" type="boolean" truevalue="-trim" falsevalue="" checked="False"
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50 label="Whether or not to allow trimming"/>
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51 <param argument="-discard" type="boolean" truevalue="-discard" falsevalue="" checked="False"
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52 label="Whether or not to discard unfixable reads. Will lose paired-end matching when discarding"/>
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53 <param argument="-noQual" type="boolean" truevalue="-noQual" falsevalue="" checked="False"
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54 label="Whether or not to ignore the quality socre"/>
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55 <param argument="-newQual" size="30" type="text" value="" optional="True"
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56 label="Quality for the bases corrected to the specified score" help="" />
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57 <param argument="-stable" type="boolean" truevalue="-stable" falsevalue="" checked="False"
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58 label="Sequentialize the sampling stage, output the same result with different runs"/>
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59 </inputs>
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60 <outputs>
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61 <data name="outfile" format_source="r"/>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="r" value="bwa-mem-fastq1.fq"/>
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66 <param name="k_select" value="smallk"/>
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67 <param name="newQual" value="12 12 0.1"/>
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68 <param name="noQual" value="True"/>
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69 <param name="stable" value="False"/>
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70 <output name="outfile" file="lighter_result1.fq"/>
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71 </test>
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72 <test>
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73 <param name="r" value="bwa-mem-fastq1.fq"/>
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74 <param name="k_select" value="bigK"/>
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75 <param name="newQual" value="20 14"/>
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76 <param name="noQual" value="False"/>
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77 <param name="stable" value="True"/>
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78 <output name="outfile" file="lighter_result2.fq"/>
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79 </test>
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80 </tests>
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81 <help>
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82 **What it does**
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83
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84 Lighter is a kmer-based error correction method for whole genome sequencing data. Lighter uses sampling
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85 (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information,
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86 Lighter can correct the reads containing sequence errors.
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87
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88 <citations>
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89 <citation type="doi">10.1186/s13059-014-0509-9</citation>
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90 </citations>
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91 </help>
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92 </tool>