Mercurial > repos > iuc > colibread_lordec

annotate lordec.xml @ 1:13c8e1ce0a15 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
author iuc
date Fri, 24 Nov 2017 12:47:46 -0500
parents dd5398cf0eeb
children 51ffe0318eea
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dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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1 <?xml version='1.0' encoding='utf-8'?>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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2 <tool profile="16.04" id="lordec" name="Lordec" version="0.6">
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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3 <description>is a set a programs for correcting sequencing errors in PacBio reads</description>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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4 <macros>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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5 <import>macros.xml</import>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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6 </macros>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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7 <requirements>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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8 <requirement type="package" version="0.6">lordec</requirement>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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9 </requirements>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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10 <command><![CDATA[
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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11
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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12 #if str( $program_type_choice.program_type ) == "correct"
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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13 lordec-correct
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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14 @lordec_inputs@
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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15 #if str( $program_type_choice.advanced_options.advanced_options_selector ) == "advanced"
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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16 -t ${program_type_choice.advanced_options.t}
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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17 -b ${program_type_choice.advanced_options.b}
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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18 -e ${program_type_choice.advanced_options.e}
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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19 -T ${program_type_choice.advanced_options.T}
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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20 #end if
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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21 -o '${corrected_read_file}'
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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22
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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23
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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24 #else if str( $program_type_choice.program_type ) == "trim"
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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25 #if $program_type_choice.split
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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26 lordec-trim-split
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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27 #else
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28 lordec-trim
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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29 #end if
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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30 -i '${program_type_choice.i}'
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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31 -o '${trimmed_reads_file}'
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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32
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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33 #else
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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34 lordec-stat
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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35 @lordec_inputs@
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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36 -S '${stat_file}'
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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37 #end if
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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38
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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39
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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40 ]]></command>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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41
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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42 <inputs>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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43
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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44 <conditional name="program_type_choice">
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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45 <param name="program_type" type="select" label="Choose Lordec program">
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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46 <option value="correct">Lordec Correct</option>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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47 <option value="trim">Lordec Trim</option>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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48 <option value="stats">Lordec Statistics</option>
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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49 </param>
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50
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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51 <when value="correct">
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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52 <expand macro="lordec_inputs" />
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53 <conditional name="advanced_options">
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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54 <param name="advanced_options_selector" type="select" label="Lordec correct advanced options">
dd5398cf0eeb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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55 <option value="default" selected="true">Default</option>
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56 <option value="advanced">Advanced</option>
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57 </param>
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58 <when value="default"></when>
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59 <when value="advanced">
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60 <param argument="-t" type="integer" label="Number of target k-mers" value="5" />
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61 <param argument="-b" type="integer" label="Maximum number of branches to explore" value="200" />
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62 <param argument="-e" type="float" label="Maximum error rate" value="0.4" />
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63 <param argument="-T" type="integer" label="Number of threads" value="1" />
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64 </when>
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65 </conditional>
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66 </when>
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67
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68 <when value="trim">
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69 <param argument="-i" type="data" format="fasta,fastq.gz,fastq" label="Long read FASTA/Q file" help="PacBio reads files" />
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70 <param name="split" type="boolean" label="Use the split option" help="Trim all weak regions and split the reads on inner weak regions" />
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71 </when>
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72
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73 <when value="stats">
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74 <expand macro="lordec_inputs" />
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75 </when>
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76
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77 </conditional>
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78
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79 </inputs>
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80
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81 <outputs>
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82 <data format="fasta" name="corrected_read_file" label="Corrected long reads with ${tool.name} on ${on_string}" >
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83 <filter>program_type_choice['program_type'] == 'correct'</filter>
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84 </data>
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85 <data format="fasta" name="trimmed_reads_file" label="Trimmed reads file with ${tool.name} on ${on_string}" >
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86 <filter>program_type_choice['program_type'] == 'trim'</filter>
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87 </data>
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88 <data format="tabular" name="stat_file" label="Stats with ${tool.name} on ${on_string}" >
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89 <filter>program_type_choice['program_type'] == 'stats'</filter>
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90 </data>
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91 </outputs>
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92
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93 <tests>
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94 <test>
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95 <conditional name="program_type_choice">
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96 <param name="program_type" value="correct" />
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97 <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
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98 <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
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99 <param name="k" value="31" />
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100 </conditional>
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101 <output name="corrected_read_file" file="lordec/corrected_reads.fa"/>
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102 </test>
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103 <test>
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104 <conditional name="program_type_choice">
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105 <param name="program_type" value="trim" />
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106 <param name="i" value="lordec/corrected_reads.fa" />
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107 </conditional>
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108 <output name="trimmed_reads_file" file="lordec/trimmed_reads.fa"/>
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109 </test>
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110 <test>
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111 <conditional name="program_type_choice">
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112 <param name="program_type" value="stats" />
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113 <param name="inputs" value="lordec/ill-test-5K-1.fa,lordec/ill-test-5K-2.fa" />
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114 <param name="i" value="lordec/coli-pacbio-test-mini.fa" />
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115 </conditional>
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116 <output name="stat_file" file="lordec/stat_file.txt"/>
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117 </test>
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118 </tests>
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119 <help><![CDATA[
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120
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121 **Lordec Correct**
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122
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123 Program for correcting sequencing errors in PacBio reads using highly accurate short reads (e.g. Illumina).
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124
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125 LoRDEC outputs the corrected reads to the given file in FASTA format. The regions that remain weak after the correction are outputted in lower case characters and the solid regions are outputted in upper case characters.
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126
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127 -------
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128
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129 **Lordec Trim**
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130
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131 Program for trimming the weak regions from the beginning and end of the corrected reads.
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132
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133 -------
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134
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135 **Lordec Statistics**
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136
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137 Program to generate statistics on solid and weak k-mers.
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138
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139 -------
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140
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141 **Web site**
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142
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143 http://www.atgc-montpellier.fr/lordec/
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144
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145
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146 ]]></help>
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147 <expand macro="citations">
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148 <citation type="doi">10.1093/bioinformatics/btu538</citation>
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149 </expand>
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150 </tool>