Mercurial > repos > iuc > stacks2_shortreads

annotate stacks_shortreads.xml @ 4:17d39bf0a63a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a"
author iuc
date Wed, 01 Sep 2021 11:23:22 +0000
parents c5d7050e4ad7
children 4e280b27a831
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ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <!-- this is essentially a copy of stacks_procrad minus the unsupported options -->
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2 <tool id="stacks2_shortreads" name="Stacks2: process shortreads" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
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3 <description>fast cleaning of randomly sheared genomic or transcriptomic data</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>macros_process.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="version_cmd"/>
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10 <command detect_errors="aggressive"><![CDATA[
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11 @FASTQ_INPUT_FUNCTIONS@
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12
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13 python '$__tool_directory__'/check_bcfile.py '$barcode' &&
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15 mkdir stacks_inputs stacks_outputs &&
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17 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
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18 $link_command
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21 process_shortreads
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23 @PROCESS_IOOPTIONS@
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24 @PROCESS_FILTER@
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25 @COMMON_ADVANCED@
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26 @RESCUE_BARCODE@
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27 @PROCESS_ADAPTER@
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29 ## advanced options not shared between shortreads and radtags
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30 $options_advanced.no_read_trimming
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31 $options_advanced.mate_pair
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32 $options_advanced.no_overhang
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34 @PROCESS_FASTQ_POSTPROC@
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35 ]]></command>
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37 <inputs>
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38 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/>
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39 <section name="options_advanced" title="advanced options" expanded="False">
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40 <expand macro="common_advanced"/>
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41 <param argument="--no_read_trimming" type="boolean" checked="false" truevalue="--no_read_trimming" falsevalue="" label="Do not trim low quality reads, just discard them"/>
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42 <param argument="--mate-pair" name="mate_pair" type="boolean" checked="false" truevalue="--mate-pair" falsevalue="" label="Raw reads are circularized mate-pair data, first read will be reverse complemented"/>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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43 <param argument="--no_overhang" type="boolean" checked="false" truevalue="--no_overhang" falsevalue="" label="Data does not contain an overhang nucleotide between barcode and seqeunce"/>
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44 <expand macro="rescue_barcode"/>
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45 <expand macro="process_adapter"/>
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46 </section>
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47 <expand macro="process_filter"/>
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48 <expand macro="process_output_types"/>
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49 </inputs>
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51 <outputs>
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52 <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file" from_work_dir="stacks_outputs/process_shortreads.log">
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53 <filter>add_log</filter>
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54 </data>
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55 <expand macro="process_outputs"/>
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56 </outputs>
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57
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58 <tests>
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59 <!-- test single end, default options -->
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60 <test expect_num_outputs="2">
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61 <param name="input_type|input_type_select" value="single"/>
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62 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
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63 <param name="input_type|barcode_encoding" value="--inline_null"/>
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64 <param name="barcode" value="procrad/barcodes"/>
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65 <param name="add_log" value="yes"/>
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66 <output name="output_log" file="shortreads/process_shortreads.out" lines_diff="4"/>
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67 <output_collection name="demultiplexed" count="40">
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68 <element name="PopA_01" file="shortreads/PopA_01.fq" ftype="fastqsanger"/>
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69 </output_collection>
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70 </test>
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71 <!-- test single end, default options -->
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72 <test expect_num_outputs="4">
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73 <param name="input_type|input_type_select" value="paired"/>
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74 <param name="input_type|fqinputs">
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75 <collection type="list:paired">
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76 <element name="reads">
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77 <collection type="paired">
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78 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger"/>
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79 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/>
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80 </collection>
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81 </element>
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82 </collection>
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83 </param>
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84 <param name="input_type|barcode_encoding" value="--inline_null"/>
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85 <param name="barcode" value="procrad/barcodes"/>
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86 <param name="capture" value="-D"/>
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87 <param name="no_read_trimming" value="--no_read_trimming"/>
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88 <param name="mate_pair" value="--mate-pair"/>
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89 <param name="no_overhang" value="--no_overhang"/>
0
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90 <param name="outype" value="gzfastq"/>
2
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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91 <param name="add_log" value="yes"/>
0
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92 <assert_command>
2
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93 <has_text text="-D"/>
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94 <has_text text="--no_read_trimming"/>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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95 <has_text text="--mate-pair"/>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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96 <has_text text="--no_overhang"/>
0
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97 </assert_command>
2
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98 <output name="output_log">
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99 <assert_contents><has_text text="ATGTAG"/></assert_contents>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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100 <assert_contents><has_text text="Sequences not recorded"/></assert_contents>
43e3eeb2e0ec "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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101 </output>
0
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102 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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103 <element name="PopA_01">
3
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104 <element name="forward" value="shortreads/PopA_01.forward.fq.gz" ftype="fastqsanger.gz" compare="diff"/>
c5d7050e4ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
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105 <element name="reverse" value="shortreads/PopA_01.reverse.fq.gz" ftype="fastqsanger.gz" compare="diff"/>
0
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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106 </element>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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107 </output_collection>
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108 <output_collection name="remaining" type="list:paired" count="40">
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109 <element name="PopA_01">
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110 <element name="forward" file="shortreads/PopA_01.rem.forward.fq.gz" ftype="fastqsanger.gz"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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111 <element name="reverse" file="shortreads/PopA_01.rem.reverse.fq.gz" ftype="fastqsanger.gz"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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112 </element>
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113 </output_collection>
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114 <output_collection name="discarded_paired" type="list:paired" count="1">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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115 <element name="reads">
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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116 <element name="forward" file="shortreads/reads.forward.fq" ftype="fastqsanger"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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117 <element name="reverse" file="shortreads/reads.forward.fq" ftype="fastqsanger"/>
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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118 </element>
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119 </output_collection>
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120 </test>
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121 </tests>
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122 <help>
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123 <![CDATA[
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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124 .. class:: infomark
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125
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126 **What it does**
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127
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128 Performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data, not for RAD data.
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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129
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130 **Help**
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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131
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132 Input files:
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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133
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134 - FASTQ
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135
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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136 - Barcode File Format
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137
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138 The barcode file is a very simple format:
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139
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140 ======= ===========
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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141 Barcode Sample name
ad7a60726fc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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142 ======= ===========
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143 ATGGGG PopA_01
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144 GGGTAA PopA_02
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145 AGGAAA PopA_03
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146 TTTAAG PopA_04
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147 GGTGTG PopA_05
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148 TGATGT PopA_06
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149 ======= ===========
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150
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151 Combinatorial barcodes are specified, one per column, separated by a tab:
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152
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153 ======== ======== ===========
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154 Barcode1 Barcode2 Sample name
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155 ======== ======== ===========
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156 CGATA ACGTA PopA_01
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157 CGGCG CGTA PopA_02
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158 GAAGC CGTA PopA_03
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159 GAGAT CGTA PopA_04
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160 CGATA AGCA PopA_05
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161 CGGCG AGCA PopA_06
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162 ======== ======== ===========
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163
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164 @STACKS_INFOS@
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165 ]]>
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166 </help>
2
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167 <expand macro="citation"/>
0
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168 </tool>