Mercurial > repos > iuc > qiime_split_libraries_fastq

annotate split_libraries_fastq.xml @ 4:3bc4d476fc29 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
author iuc
date Fri, 04 Aug 2017 18:20:14 -0400
parents c80794803b3f
children f3f3afb3b221
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c80794803b3f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool id="qiime_split_libraries_fastq" name="Split fastq libraries" version="@WRAPPER_VERSION@.0">
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2 <description> to performs demultiplexing of Fastq sequence data (split_libraries_fastq)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>split_libraries_fastq.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 split_libraries_fastq.py
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10 #set $seq_files = ''
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11 #set $sep = ''
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12 #for $file in $sequence_read_fps
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13 #set $seq_files += $sep + str($file)
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14 #set $sep = ','
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15 #end for
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16 --sequence_read_fps '$seq_files'
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17
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18 -o split_libraries
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19
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20 #set $mapping_files = ''
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21 #set $sep = ''
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22 #for $file in $mapping_fps
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23 #set $mapping_files += $sep + str($file)
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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24 #set $sep = ','
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25 #end for
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26 #if $mapping_files != 'None'
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27 --mapping_fps '$mapping_files'
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28 #end if
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29
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30 #set $barcode_files = ''
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31 #set $sep = ''
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32 #for $file in $barcode_read_fps
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33 #set $barcode_files += $sep + str($file)
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34 #set $sep = ','
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35 #end for
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36 #if $barcode_files != 'None'
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37 --barcode_read_fps '$barcode_files'
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38 #end if
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39
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40 $store_qual_scores
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41 #if str($sample_ids) != ''
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42 --sample_ids '$sample_ids'
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43 #end if
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44 $store_demultiplexed_fastq
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45 $retain_unassigned_reads
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46
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47 --max_bad_run_length '$max_bad_run_length'
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48 --min_per_read_length_fraction '$min_per_read_length_fraction'
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49 --sequence_max_n '$sequence_max_n'
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50 --start_seq_id '$start_seq_id'
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51 $rev_comp_barcode
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52 $rev_comp_mapping_barcodes
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53 $rev_comp
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54 --phred_quality_threshold '$phred_quality_threshold'
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55 #if str( $barcode.barcode_type ) != "custom_length"
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56 --barcode_type '$barcode.barcode_type'
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57 #else
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58 --barcode_type '$barcode.barcode_length'
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59 #end if
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60 --max_barcode_errors '$max_barcode_errors'
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61 $phred_offset
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62 ]]></command>
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63 <inputs>
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64 <param argument="--sequence_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" multiple="true" label="Input fastq files"/>
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65 <param argument="--mapping_fps" type="data" format="txt,tabular,tsv,csv" multiple="true" optional="true" label="Metadata mapping files"/>
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66 <param argument="--barcode_read_fps" type="data" format="fastq,fastqsanger,fastqsolexa" multiple="true" optional="true" label="Barcode read files"/>
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67 <param argument="--store_qual_scores" type="boolean" truevalue="--store_qual_scores" falsevalue="" checked="false" label="Store quality strings in files?"/>
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68 <param argument="--sample_ids" type="text" optional="true" label="Comma-separated list of samples ids to be applied to all sequences" help="It must be one per input file path (used when data is not multiplexed)"/>
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69 <param argument="--store_demultiplexed_fastq" type="boolean" truevalue="--store_demultiplexed_fastq" falsevalue="" checked="false" label="Write demultiplexed fastq files?"/>
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70 <param argument="--retain_unassigned_reads" type="boolean" truevalue="--retain_unassigned_reads" falsevalue="" checked="false" label="Retain sequences which don’t map to a barcode in the mapping file?" help="Sample ID will be 'Unassigned'"/>
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71 <param argument="--max_bad_run_length" type="integer" value="3" label="Maximum number of consecutive low quality base calls allowed before truncating a read"/>
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72 <param argument="--min_per_read_length_fraction" type="float" value="0.75" label="Minimum number of consecutive high quality base calls to include a read (per single end read) as a fraction of the input read length"/>
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73 <param argument="--sequence_max_n" type="integer" value="0" label="Maximum number of N characters allowed in a sequence to retain it" help="This is applied after quality trimming, and is total over combined paired end reads if applicable"/>
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74 <param argument="--start_seq_id" type="integer" value="0" label="Start seq_ids as ascending integers beginning with start_seq_id"/>
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75 <param argument="--rev_comp_barcode" type="boolean" truevalue="--rev_comp_barcode" falsevalue="" checked="false" label="Reverse complement barcode reads before lookup?"/>
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76 <param argument="--rev_comp_mapping_barcodes" type="boolean" truevalue="--rev_comp_mapping_barcodes" falsevalue="" checked="false" label="Reverse complement barcode in mapping before lookup?" help="It is useful if barcodes in mapping file are reverse complements of golay codes"/>
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77 <param argument="--rev_comp" type="boolean" truevalue="--rev_comp" falsevalue="" checked="false" label="Reverse complement sequence before writing to output file?"/>
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78 <param argument="--phred_quality_threshold" type="integer" value="3" label="Maximum unacceptable Phred quality score" help="E.g., for Q20 and better, 19 must be specified"/>
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79 <conditional name="barcode">
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80 <param argument="--barcode_type" type="select" label="Type of barcode">
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81 <option value="hamming_8">hamming_8</option>
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82 <option value="golay_12" selected="true">golay_12</option>
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83 <option value="variable_length">variable_length (disable any barcode correction)</option>
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84 <option value="custom_length">Custom length</option>
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85 <option value="not-barcoded">Data not barcoded</option>
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86 </param>
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87 <when value="hamming_8"/>
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88 <when value="golay_12"/>
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89 <when value="variable_length"/>
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90 <when value="custom_length">
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91 <param name="barcode_length" type="integer" value="4" label="Barcode length"/>
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92 </when>
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93 <when value="not-barcoded"/>
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94 </conditional>
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95 <param argument="--max_barcode_errors" type="float" value="1.5" label="Maximum number of errors in barcode"/>
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96 <param argument="--phred_offset" type="select" label="Ascii offset to use when decoding phred scores">
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97 <option value="--phred_offset 33">33</option>
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98 <option value="--phred_offset 64">64</option>
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99 <option value="" selected="true">Automatically determined</option>
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100 </param>
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101 </inputs>
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102 <outputs>
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103 <data name="log" format="txt" from_work_dir="split_libraries/split_library_log.txt" label="${tool.name} on ${on_string}: log"/>
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104 <data name="histograms" format="tabular" from_work_dir="split_libraries/histograms.txt" label="${tool.name} on ${on_string}: histograms"/>
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105 <data name="seqs" format="fasta" from_work_dir="split_libraries/seqs.fna" label="${tool.name} on ${on_string}: sequences"/>
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106 <data name="seqs_qual" format="qual" from_work_dir="split_libraries/seqs.qual" label="${tool.name} on ${on_string}: sequence qualities">
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107 <filter>store_qual_scores is True</filter>
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108 </data>
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109 <data name="seqs_fastq" format="fastq" from_work_dir="split_libraries/seqs.fastq" label="${tool.name} on ${on_string}: demultiplexed sequences (fastq)">
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110 <filter>store_demultiplexed_fastq is True</filter>
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111 </data>
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112 </outputs>
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113 <tests>
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114 <test>
4
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115 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz"/>
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116 <param name="mapping_fps" value="split_libraries_fastq/map.txt"/>
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117 <param name="barcode_read_fps" value="split_libraries_fastq/lane1_barcode.fastq.gz"/>
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118 <param name="store_qual_scores" value=""/>
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119 <param name="store_demultiplexed_fastq" value=""/>
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120 <param name="retain_unassigned_reads" value=""/>
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121 <param name="max_bad_run_length" value="3"/>
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122 <param name="min_per_read_length_fraction" value="0.75"/>
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123 <param name="sequence_max_n" value="0"/>
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124 <param name="start_seq_id" value="0"/>
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125 <param name="rev_comp_barcode" value=""/>
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126 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
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127 <param name="rev_comp" value=""/>
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128 <param name="phred_quality_threshold" value="19"/>
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129 <conditional name="barcode">
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130 <param name="barcode_type" value="golay_12"/>
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131 </conditional>
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132 <param name="max_barcode_errors" value="1.5"/>
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133 <param name="phred_offset" value=""/>
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134 <output name="log">
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135 <assert_contents>
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136 <has_text text="Median sequence length: 151.00"></has_text>
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137 <has_text text="s41"></has_text>
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138 <has_text text="s122"></has_text>
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139 </assert_contents>
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140 </output>
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141 <output name="seqs" ftype="fasta">
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142 <assert_contents>
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143 <has_text text="s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
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144 <has_text text="s26_84 M00176:17:000000000-A0CNA:1:1:18075:1844 1:N:0:0 orig_bc=AGGGTTCCAGTT new_bc=AGGGTTCCAGTT bc_diffs=0"></has_text>
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145 </assert_contents>
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146 </output>
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147 <output name="histograms">
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148 <assert_contents>
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149 <has_text text="Length"></has_text>
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150 <has_text text="127.0"></has_text>
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151 <has_text text="157.0"></has_text>
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152 </assert_contents>
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153 </output>
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154 </test>
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155 <test>
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156 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz"/>
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157 <param name="mapping_fps" value="split_libraries_fastq/map.txt"/>
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158 <param name="barcode_read_fps" value="split_libraries_fastq/lane1_barcode.fastq.gz"/>
0
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159 <param name="store_qual_scores" value="--store_qual_scores"/>
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160 <param name="store_demultiplexed_fastq" value="--store_demultiplexed_fastq"/>
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161 <param name="retain_unassigned_reads" value=""/>
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162 <param name="max_bad_run_length" value="3"/>
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163 <param name="min_per_read_length_fraction" value="0.75"/>
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164 <param name="sequence_max_n" value="0"/>
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165 <param name="start_seq_id" value="0"/>
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166 <param name="rev_comp_barcode" value=""/>
4
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167 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
0
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168 <param name="rev_comp" value=""/>
4
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169 <param name="phred_quality_threshold" value="19"/>
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170 <conditional name="barcode">
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171 <param name="barcode_type" value="golay_12"/>
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172 </conditional>
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173 <param name="max_barcode_errors" value="1.5"/>
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174 <param name="phred_offset" value=""/>
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175 <output name="log">
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176 <assert_contents>
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177 <has_text text="Median sequence length: 151.00"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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178 <has_text text="s41"></has_text>
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179 <has_text text="s122"></has_text>
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180 </assert_contents>
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181 </output>
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182 <output name="seqs" ftype="fasta">
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183 <assert_contents>
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184 <has_text text="s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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185 <has_text text="s107_6 M00176:17:000000000-A0CNA:1:1:15276:1779 1:N:0:0 orig_bc=ATCTCCTCTCCA new_bc=ATCTCCTCTCCA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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186 </assert_contents>
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187 </output>
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188 <output name="seqs_fastq" ftype="fastq">
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189 <assert_contents>
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190 <has_text text="@s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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191 <has_text text="@s107_6 M00176:17:000000000-A0CNA:1:1:15276:1779 1:N:0:0 orig_bc=ATCTCCTCTCCA new_bc=ATCTCCTCTCCA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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192 </assert_contents>
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193 </output>
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194 <output name="seqs_qual" ftype="qual">
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195 <assert_contents>
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196 <has_text text="s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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197 <has_text text="s107_6 M00176:17:000000000-A0CNA:1:1:15276:1779 1:N:0:0 orig_bc=ATCTCCTCTCCA new_bc=ATCTCCTCTCCA bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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198 </assert_contents>
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199 </output>
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200 <output name="histograms">
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201 <assert_contents>
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202 <has_text text="Length"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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203 <has_text text="127.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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204 <has_text text="157.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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205 </assert_contents>
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206 </output>
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207 </test>
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208 <test>
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209 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz,split_libraries_fastq/lane2_read1.fastq.gz"/>
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210 <param name="mapping_fps" value="split_libraries_fastq/map.txt,split_libraries_fastq/map.txt"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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211 <param name="barcode_read_fps" value="split_libraries_fastq/lane1_barcode.fastq.gz,split_libraries_fastq/lane2_barcode.fastq.gz"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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212 <param name="store_qual_scores" value=""/>
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213 <param name="store_demultiplexed_fastq" value=""/>
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214 <param name="retain_unassigned_reads" value=""/>
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215 <param name="max_bad_run_length" value="3"/>
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216 <param name="min_per_read_length_fraction" value="0.75"/>
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217 <param name="sequence_max_n" value="0"/>
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218 <param name="start_seq_id" value="0"/>
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219 <param name="rev_comp_barcode" value=""/>
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220 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
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221 <param name="rev_comp" value=""/>
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222 <param name="phred_quality_threshold" value="19"/>
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223 <conditional name="barcode">
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224 <param name="barcode_type" value="golay_12"/>
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225 </conditional>
0
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226 <param name="max_barcode_errors" value="1.5"/>
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227 <param name="phred_offset" value=""/>
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228 <output name="log">
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229 <assert_contents>
4
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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230 <has_text text="Median sequence length: 151.00"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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231 <has_text text="s41"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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232 <has_text text="s122"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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233 </assert_contents>
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234 </output>
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235 <output name="seqs" ftype="fasta">
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236 <assert_contents>
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237 <has_text text="s161_0 M00176:17:000000000-A0CNA:1:1:16738:1773 1:N:0:0 orig_bc=CTCGCTTCACTT new_bc=CTCGCTTCACTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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238 <has_text text="s26_84 M00176:17:000000000-A0CNA:1:1:18075:1844 1:N:0:0 orig_bc=AGGGTTCCAGTT new_bc=AGGGTTCCAGTT bc_diffs=0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
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239 </assert_contents>
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240 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
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241 <output name="histograms">
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242 <assert_contents>
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243 <has_text text="Length"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
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244 <has_text text="127.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
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245 <has_text text="157.0"></has_text>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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246 </assert_contents>
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247 </output>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
iuc
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248 </test>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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249 <test>
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iuc
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250 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz"/>
3bc4d476fc29 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
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251 <param name="store_qual_scores" value=""/>
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252 <param name="sample_ids" value="my.sample.1"/>
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253 <param name="store_demultiplexed_fastq" value=""/>
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254 <param name="retain_unassigned_reads" value=""/>
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255 <param name="max_bad_run_length" value="3"/>
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256 <param name="min_per_read_length_fraction" value="0.75"/>
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257 <param name="sequence_max_n" value="0"/>
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258 <param name="start_seq_id" value="0"/>
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259 <param name="rev_comp_barcode" value=""/>
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260 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
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261 <param name="rev_comp" value=""/>
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262 <param name="phred_quality_threshold" value="19"/>
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263 <conditional name="barcode">
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264 <param name="barcode_type" value="not-barcoded"/>
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265 </conditional>
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266 <param name="phred_offset" value=""/>
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267 <output name="log">
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268 <assert_contents>
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269 <has_text text="Median sequence length: 151.00"></has_text>
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270 <has_text text="my.sample.1"></has_text>
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271 <has_text text="Total number seqs written"></has_text>
0
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272 </assert_contents>
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273 </output>
4
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274 <output name="seqs" ftype="fasta">
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275 <assert_contents>
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276 <has_text text="my.sample.1_0 M00176:17:000000000-A0CNA:1:1:15487:1773 1:N:0:0 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0"></has_text>
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277 <has_text text="my.sample.1_12 M00176:17:000000000-A0CNA:1:1:14889:1778 1:N:0:0 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0"></has_text>
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278 </assert_contents>
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279 </output>
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280 <output name="histograms">
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281 <assert_contents>
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282 <has_text text="Length"></has_text>
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283 <has_text text="124.0"></has_text>
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284 <has_text text="154.0"></has_text>
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285 </assert_contents>
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286 </output>
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287 </test>
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288 <test>
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289 <param name="sequence_read_fps" value="split_libraries_fastq/lane1_read1.fastq.gz,split_libraries_fastq/lane2_read1.fastq.gz"/>
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290 <param name="store_qual_scores" value=""/>
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291 <param name="sample_ids" value="my.sample.1,my.sample.2"/>
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292 <param name="store_demultiplexed_fastq" value=""/>
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293 <param name="retain_unassigned_reads" value=""/>
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294 <param name="max_bad_run_length" value="3"/>
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295 <param name="min_per_read_length_fraction" value="0.75"/>
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296 <param name="sequence_max_n" value="0"/>
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297 <param name="start_seq_id" value="0"/>
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298 <param name="rev_comp_barcode" value=""/>
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299 <param name="rev_comp_mapping_barcodes" value="--rev_comp_mapping_barcodes"/>
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300 <param name="rev_comp" value=""/>
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301 <param name="phred_quality_threshold" value="19"/>
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302 <conditional name="barcode">
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303 <param name="barcode_type" value="not-barcoded"/>
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304 </conditional>
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305 <param name="phred_offset" value=""/>
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306 <output name="log">
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307 <assert_contents>
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308 <has_text text="Median sequence length: 151.00"></has_text>
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309 <has_text text="my.sample.1"></has_text>
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310 <has_text text="Total number seqs written"></has_text>
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311 </assert_contents>
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312 </output>
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313 <output name="seqs" ftype="fasta">
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314 <assert_contents>
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315 <has_text text="my.sample.1_0 M00176:17:000000000-A0CNA:1:1:15487:1773 1:N:0:0 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0"></has_text>
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316 <has_text text="my.sample.1_12 M00176:17:000000000-A0CNA:1:1:14889:1778 1:N:0:0 orig_bc=AAAAAAAAAAAA new_bc=AAAAAAAAAAAA bc_diffs=0"></has_text>
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317 </assert_contents>
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318 </output>
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319 <output name="histograms">
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320 <assert_contents>
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321 <has_text text="Length"></has_text>
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322 <has_text text="124.0"></has_text>
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323 <has_text text="154.0"></has_text>
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324 </assert_contents>
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325 </output>
0
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326 </test>
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327 </tests>
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328 <help><![CDATA[
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329 **What it does**
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330
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331 This tool performs demultiplexing of Fastq sequence data where barcodes and sequences are contained in two separate fastq files (common on Illumina runs).
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332
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333 More information about this tool is available on
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334 `QIIME documentation <http://qiime.org/scripts/split_libraries_fastq.html>`_.
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335 ]]></help>
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336 <citations>
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337 <expand macro="citations"/>
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338 </citations>
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339 </tool>