Mercurial > repos > mvdbeek > dedup_hash

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planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
author mvdbeek
date Wed, 23 Nov 2016 07:49:05 -0500
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f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
mvdbeek
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1 <tool id="dedup_hash" name="Deduplicate FASTQ files" version="0.1.1">
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2 <description>with fast and memory-efficient sequence hashes</description>
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3 <requirements>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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4 <requirement type="package" version="0.150.1">smhasher</requirement>
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5 </requirements>
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6 <command><![CDATA[
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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7 python '$__tool_directory__/dedup_hash/dedup_hash.py'
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mvdbeek
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8 #if str($readtype.single_or_paired) == "se":
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9 --r1_in '${readtype.input_single}'
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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10 --r1_out '$output_single'
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11 #elif str($readtype.single_or_paired) == "pe_sep":
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12 --r1_in '${readtype.input_paired1}'
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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13 --r2_in '${readtype.input_paired2}'
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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14 --r1_out '$output_paired1'
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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15 --r2_out '$output_paired2'
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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16 #else
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17 --r1_in '${readtype.input_paired.forward}'
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18 --r2_in '${readtype.input_paired.reverse}'
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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19 --r1_out '${output_paired_coll.forward}'
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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20 --r2_out '${output_paired_coll.reverse}'
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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21 #end if
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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22 $compress_fastq
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23 ]]></command>
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24 <inputs>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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25 <conditional name="readtype">
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26 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">
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27 <option value="se" selected="true">Single-end</option>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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28 <option value="pe_sep">Paired-end (two separate input files)</option>
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29 <option value="pe_collection">Paired-end (as collection)</option>
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30 </param>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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31 <when value="se">
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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32 <param format="fastq,fastq.gz" name="input_single" type="data" label="Single-end FASTQ reads" help="(-f)" />
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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33 </when>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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34 <when value="pe_sep">
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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35 <param format="fastq,fastq.gz" name="input_paired1" type="data" label="Paired-end forward strand FASTQ reads" help="(-f)" />
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36 <param format="fastq,fastq.gz" name="input_paired2" type="data" label="Paired-end reverse strand FASTQ reads" help="(-r)" />
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37 </when>
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38 <when value="pe_collection">
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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39 <param name="input_paired" format="fastq,fastq.gz" type="data_collection" collection_type="paired" label="Paired-end FASTQ reads as paired collection" />
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40 </when>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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41 </conditional>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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42 <param name="compress_fastq" type="boolean" checked="true" truevalue="--write_gzip" falsevalue="" label="Produce compressed fastq?"/>
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43 </inputs>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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44 <outputs>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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45 <data name="output_single" format="fastq" label="Single-end output of ${tool.name} on ${on_string}">
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46 <filter>readtype['single_or_paired'] == 'se'</filter>
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47 <change_format>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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48 <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
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49 </change_format>
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50 </data>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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51 <data name="output_paired1" format="fastq" label="Paired-end forward strand output of ${tool.name} on ${on_string}">
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52 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
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53 <change_format>
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54 <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
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55 </change_format>
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56 </data>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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57 <data name="output_paired2" format="fastq" label="Paired-end reverse strand output of ${tool.name} on ${on_string}">
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58 <filter>readtype['single_or_paired'] == 'pe_sep'</filter>
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59 <change_format>
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60 <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
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61 </change_format>
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62 </data>
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63 <collection name="output_paired_coll" type="paired" structured_like="readtype.pe_collection" label="Paired-end output of ${tool.name} on ${on_string}">
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64 <filter>readtype['single_or_paired'] == 'pe_collection'</filter>
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65 <data name="forward" format="fastq">
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66 <change_format>
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67 <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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68 </change_format>
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69 </data>
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70 <data name="reverse" format="fastq">
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71 <change_format>
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72 <when input="compress_fastq" value="--write_gzip" format="fastq.gz" />
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73 </change_format>
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74 </data>
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75 </collection>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="single_or_paired" value="pe_sep"/>
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80 <param name="input_paired1" value="r1.fastq.gz" ftype="fastq.gz"/>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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81 <param name="input_paired2" value="r2.fastq.gz" ftype="fastq.gz"/>
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82 <param name="compress_fastq" value="--write_gzip"/>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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83 <output name="output_paired1" file="r1_dedup.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
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84 <output name="output_paired2" file="r2_dedup.fastq.gz" ftype="fastq.gz" compare="sim_size"/>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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85 </test>
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86 <test>
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87 <param name="single_or_paired" value="pe_sep"/>
f33e9e6a6c88 planemo upload for repository https://github.com/mvdbeek/dedup_hash commit 367da560c5924d56c39f91ef9c731e523825424b-dirty
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88 <param name="input_paired1" value="r1.fastq" ftype="fastq"/>
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89 <param name="input_paired2" value="r2.fastq" ftype="fastq"/>
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90 <param name="compress_fastq" value=""/>
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91 <output name="output_paired1" file="r1_dedup.fastq" ftype="fastq"/>
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92 <output name="output_paired2" file="r2_dedup.fastq" ftype="fastq"/>
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93 </test>
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94 </tests>
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95 <help> <![CDATA[
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96 **Deduplicate paired fastq** is a fast and memory-efficient tool for removal of duplicates in paired short DNA sequence reads in fastq format.
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97 It identifies duplicates by concatenating the sequence of a readpair and calculating a short hash that uniquely identifies the concatenated sequence.
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98 Sequences that are not unique (i.e a hash of the concatenated sequence has been seen previously) are being discarded.
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99
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100 Compared to fastuniq this tool requires only a fraction of the memory, but does not identify pairs that are identical,
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101 except for a switch of R1 and R2. Such reads may nevertheless align to different places based on the seed-searching of the aligner,
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102 so this may or may not be a problem for your application.
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103
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104 Fastuniq consumed 76 GB of memory and took 4:01.52 on a typical dataset of 100nt 25 x 10^6 paired end reads,
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105 while this tool took 4.7GB of memory and 3:23.27 for the same dataset.
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106
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107 Both tools produced the exact same result, arguing that, at least before quality and/or adapter trimming,
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108 the previously mentioned limitations are of theoretical concern.
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109
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110 ]]> </help>
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111 <citations>
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112 <citation type="doi">doi:10.1371/journal.pone.0052249</citation>
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113 </citations>
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114 </tool>