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annotate rcorrector.xml @ 0:9a0b65ad3c84 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
author iuc
date Thu, 13 Sep 2018 07:00:00 -0400
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9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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1 <tool id="rcorrector" name="RNA-seq Rcorrector" version="1.0.3">
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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2 <description>a kmer-based error correction method for RNA-seq data</description>
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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3 <requirements>
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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4 <requirement type="package" version="1.0.3">rcorrector</requirement>
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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5 </requirements>
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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6 <command detect_errors="exit_code"><![CDATA[
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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7 #if $library.lib == "single":
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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8 ln -s '$library.input1' input_1.fq &&
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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9 #end if
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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10 #if $library.lib == "paired":
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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11 ln -s '$library.input1' input_1.fq && ln -s '$library.input2' input_2.fq &&
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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12 #end if
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13 run_rcorrector.pl
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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14 #if $library.lib == "single":
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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15 -s input_1.fq
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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16 #end if
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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17 #if $library.lib == "paired":
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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18 -1 input_1.fq -2 input_2.fq
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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19 #end if
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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20 -k '$advanced.kmers' -t \${GALAXY_SLOTS:-4} -maxcorK '$advanced.maxcorK' -wk '$advanced.wk' -ek '$advanced.ek' -od output_file_directory
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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21
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22 #if $library.lib == "paired":
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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23 #if $library.filter:
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24 && python '$__tool_directory__/FilterUncorrectabledPEfastq.py'
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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25 -1 output_file_directory/input_1.cor.fq -2 output_file_directory/input_2.cor.fq -o fixed 2>&1 > rmunfixable.log && cat rmunfixable.log
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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26 #end if
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27 #end if
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28 ]]></command>
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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29 <inputs>
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30 <conditional name="library">
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31 <param name="lib" type="select" label="Is this library paired- or single-end?">
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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32 <option value="single">single</option>
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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33 <option value="paired" selected="True">paired</option>
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34 </param>
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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35 <when value="single">
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36 <param type="data" name="input1" label="FastQ file" format="fastq,fastqsanger" />
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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37 </when>
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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38 <when value="paired">
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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39 <param type="data" name="input1" label="FastQ file R1 (left)" format="fastq,fastqsanger" />
9a0b65ad3c84 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector commit eba2cb86379f6ee6899a1141226e191c63fadfa6
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40 <param type="data" name="input2" label="FastQ file R2 (right)" format="fastq,fastqsanger" />
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41 <param name="filter" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Filter uncorrectable reads" help="This will run FilterUncorrectabledPEfastq and remove uncorrectable reads."/>
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42 </when>
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43 </conditional>
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44 <conditional name="advanced">
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45 <param name="adv" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Additional options"/>
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46 <when value="TRUE">
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47 <param name="kmers" label="kmer length" value="23" max="32" type="integer" help="(smaller 33, default: 23)"/>
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48 <param name="maxcorK" label="max correction within k-bp window" value="4" type="integer" help="the maximum number of correction within k-bp window (default: 4)"/>
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49 <param name="wk" label="estimate weak kmer count" value="0.95" type="float" help="the proportion of kmers that are used to estimate weak kmer count threshold, lower for more divergent genome (default: 0.95)"/>
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50 <param name="ek" label="expected number of kmers" value="100000000" type="integer" help="expected_number_of_kmers: does not affect the correctness of program but affect the memory usage (default: 100000000)"/>
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51 </when>
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52 <when value="FALSE">
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53 <param name="kmers" value="23" type="hidden"/>
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54 <param name="maxcorK" value="4" type="hidden"/>
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55 <param name="wk" value="0.95" type="hidden"/>
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56 <param name="ek" value="100000000" type="hidden"/>
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57 </when>
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58 </conditional>
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59 </inputs>
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60 <outputs>
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61 <data name="output1" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="output_file_directory/input_1.cor.fq">
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62 <filter>library['lib'] == 'single'</filter>
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63 </data>
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64 <data name="output2" format="fastq" label="${tool.name} on ${on_string}: cor R1" from_work_dir="output_file_directory/input_1.cor.fq">
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65 <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
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66 </data>
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67 <data name="output3" format="fastq" label="${tool.name} on ${on_string}: cor R2" from_work_dir="output_file_directory/input_2.cor.fq">
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68 <filter>library['lib'] == 'paired' and library['filter'] is False</filter>
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69 </data>
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70 <data name="output4" format="fastq" label="${tool.name} on ${on_string}: fixed R1" from_work_dir="fixed_input_1.cor.fq">
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71 <filter>library['lib'] == 'paired' and library['filter']</filter>
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72 </data>
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73 <data name="output5" format="fastq" label="${tool.name} on ${on_string}: fixed R2" from_work_dir="fixed_input_2.cor.fq">
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74 <filter>library['lib'] == 'paired' and library['filter']</filter>
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75 </data>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <conditional name="library">
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80 <param name="lib" value="paired"/>
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81 <param name="input1" value="sample_read1.fq" ftype="fastq"/>
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82 <param name="input2" value="sample_read2.fq" ftype="fastq"/>
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83 </conditional>
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84 <conditional name="advanced">
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85 <param name="kmers" value="23"/>
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86 <param name="maxcorK" value="4"/>
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87 <param name="wk" value="0.95"/>
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88 <param name="ek" value="100000000"/>
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89 </conditional>
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90 <output name="output2" file="sample_read1.cor.fq" ftype="fastq"/>
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91 <output name="output3" file="sample_read2.cor.fq" ftype="fastq"/>
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92 </test>
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93 <test>
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94 <conditional name="library">
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95 <param name="lib" value="paired"/>
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96 <param name="input1" value="sample_read1.fq" ftype="fastq"/>
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97 <param name="input2" value="sample_read2.fq" ftype="fastq"/>
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98 <param name="filter" value="TRUE"/>
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99 </conditional>
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100 <conditional name="advanced">
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101 <param name="kmers" value="23"/>
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102 <param name="maxcorK" value="4"/>
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103 <param name="wk" value="0.95"/>
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104 <param name="ek" value="100000000"/>
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105 </conditional>
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106 <output name="output2" file="fixed_sample_read1.cor.fq" compare="sim_size"/>
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107 <output name="output3" file="fixed_sample_read2.cor.fq" compare="sim_size"/>
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108 </test>
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109 </tests>
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110 <help><![CDATA[
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111
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112 What is Rcorrector?
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113
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114 Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.
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115 Rcorrector can also be applied to other type of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.
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116
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117 Uncorrectable paired-end reads can be removed using FilterUncorrectabledPEfastq.
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118
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119 More informations, see citations.
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120
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121 ]]>
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122 </help>
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123 <citations>
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124 <citation type="doi">10.1186/s13742-015-0089-y</citation>
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125 <citation type="bibtex">
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126 @misc{githubFilterUncorrectabledPEfastq,
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127 author = {Adam H. Freedman},
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128 year = {2016},
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129 title = {FilterUncorrectabledPEfastq},
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130 publisher = {GitHub},
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131 journal = {GitHub repository},
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132 url = {https://github.com/harvardinformatics/TranscriptomeAssemblyTools/blob/master/FilterUncorrectabledPEfastq.py}
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133 }
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134 </citation>
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135 </citations>
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136 </tool>