Mercurial > repos > bgruening > lighter
annotate lighter.xml @ 2:b4d3d0643b0a draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/lighter commit d52414cda24443e19c511251e0fac4d49d97f914
author | bgruening |
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date | Tue, 12 Mar 2024 11:21:16 +0000 |
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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"> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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2 <description>can correct the reads containing sequence errors</description> |
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b4d3d0643b0a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/lighter commit d52414cda24443e19c511251e0fac4d49d97f914
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3 <xrefs> |
b4d3d0643b0a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/lighter commit d52414cda24443e19c511251e0fac4d49d97f914
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4 <xref type="bio.tools">lighter</xref> |
b4d3d0643b0a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/lighter commit d52414cda24443e19c511251e0fac4d49d97f914
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5 </xrefs> |
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89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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6 <requirements> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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7 <requirement type="package" version="1.1.1">lighter</requirement> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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8 </requirements> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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9 <command><![CDATA[ |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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10 lighter |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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11 #for $file in $r: |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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12 -r $file |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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13 #end for |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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14 #if str($kmer.k_select) == "smallk": |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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15 -k $kmer.k_parameter_string |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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16 #elif str($kmer.k_select) == "bigK": |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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17 -K $kmer.K_parameter_string |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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18 #end if |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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19 -od ./ |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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20 -t \${GALAXY_SLOTS:-4} |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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21 #if $maxcor: |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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22 -maxcor $maxcor |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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23 #end if |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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24 $trim |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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25 $discard |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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26 $noQual |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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27 #if $newQual: |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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28 -newQual '$newQual' |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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29 #end if |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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30 $stable |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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31 > $outfile |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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32 ]]> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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33 </command> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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34 <inputs> |
2
b4d3d0643b0a
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/lighter commit d52414cda24443e19c511251e0fac4d49d97f914
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35 <param argument="-r" multiple="True" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input file"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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36 <conditional name="kmer"> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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37 <param name="k_select" type="select" label="Do you want k or K?"> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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38 <option value="smallk">small k</option> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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39 <option value="bigK">big K</option> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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40 </param> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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41 <when value="smallk"> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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42 <param name="k_parameter_string" size="30" type="text" value="13 20 0.2" label="type in 3 parameters" |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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43 help="(—k kmer_length genome_size alpha)" /> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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44 </when> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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45 <when value="bigK"> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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46 <param name="K_parameter_string" size="30" type="text" value="13 20" label="type in 2 parameters" |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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47 help="(—K kmer_length genome_size)" /> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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48 </when> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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49 </conditional> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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50 <param argument="-maxcor" type="integer" value="4" optional="True" |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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51 label="Maximum number of correction for within a kmer length window" help=""/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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52 <param argument="-trim" type="boolean" truevalue="-trim" falsevalue="" checked="False" |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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53 label="Whether or not to allow trimming"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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54 <param argument="-discard" type="boolean" truevalue="-discard" falsevalue="" checked="False" |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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55 label="Whether or not to discard unfixable reads. Will lose paired-end matching when discarding"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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56 <param argument="-noQual" type="boolean" truevalue="-noQual" falsevalue="" checked="False" |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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57 label="Whether or not to ignore the quality socre"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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58 <param argument="-newQual" size="30" type="text" value="" optional="True" |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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59 label="Quality for the bases corrected to the specified score" help="" /> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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60 <param argument="-stable" type="boolean" truevalue="-stable" falsevalue="" checked="False" |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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61 label="Sequentialize the sampling stage, output the same result with different runs"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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62 </inputs> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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63 <outputs> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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64 <data name="outfile" format_source="r"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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65 </outputs> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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66 <tests> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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67 <test> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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68 <param name="r" value="bwa-mem-fastq1.fq"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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69 <param name="k_select" value="smallk"/> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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70 <param name="newQual" value="12 12 0.1"/> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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71 <param name="noQual" value="True"/> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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72 <param name="stable" value="False"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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73 <output name="outfile" file="lighter_result1.fq"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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74 </test> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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75 <test> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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76 <param name="r" value="bwa-mem-fastq1.fq"/> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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77 <param name="k_select" value="bigK"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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78 <param name="newQual" value="20 14"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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79 <param name="noQual" value="False"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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80 <param name="stable" value="True"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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81 <output name="outfile" file="lighter_result2.fq"/> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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82 </test> |
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83 </tests> |
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84 <help> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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85 **What it does** |
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86 |
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87 Lighter is a kmer-based error correction method for whole genome sequencing data. Lighter uses sampling |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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88 (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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89 Lighter can correct the reads containing sequence errors. |
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90 </help> |
0
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91 <citations> |
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planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
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92 <citation type="doi">10.1186/s13059-014-0509-9</citation> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
bgruening
parents:
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93 </citations> |
89b453176d05
planemo upload for repository https://github.com/mourisl/Lighter commit 5f1e53104d11817b9f1f93c4df17b77c80bd7472
bgruening
parents:
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94 </tool> |