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annotate preprocess.xml @ 0:59bc96331073 draft default tip

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
author frogs
date Thu, 28 Feb 2019 10:14:49 -0500
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59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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1 <?xml version="1.0"?>
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2 <!--
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3 # Copyright (C) 2015 INRA
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4 #
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5 # This program is free software: you can redistribute it and/or modify
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6 # it under the terms of the GNU General Public License as published by
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7 # the Free Software Foundation, either version 3 of the License, or
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8 # (at your option) any later version.
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9 #
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10 # This program is distributed in the hope that it will be useful,
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11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 # GNU General Public License for more details.
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14 #
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15 # You should have received a copy of the GNU General Public License
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16 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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17 -->
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18 <tool id="FROGS_preprocess" name="FROGS Pre-process" version="3.1">
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19 <description>merging, denoising and dereplication.</description>
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20 <requirements>
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21 <requirement type="package" version="3.1.0">frogs</requirement>
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22 </requirements>
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23 <stdio>
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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24 <exit_code range="1:" />
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25 <exit_code range=":-1" />
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26 </stdio>
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27 <command>
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28 preprocess.py $sequencer_type.sequencer_selected
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29 --output-dereplicated $dereplicated_file --output-count $count_file --summary $summary_file
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30 --nb-cpus \${GALAXY_SLOTS:-1}
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31 --min-amplicon-size $sequencer_type.min_amplicon_size --max-amplicon-size $sequencer_type.max_amplicon_size
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32
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33 #if $sequencer_type.sequencer_selected == "illumina"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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34 #if $sequencer_type.sequencing_protocol.sequencing_protocol_selected == "standard"
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35 --five-prim-primer $sequencer_type.sequencing_protocol.five_prim_primer --three-prim-primer $sequencer_type.sequencing_protocol.three_prim_primer
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36 #else
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37 --without-primers
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38 #end if
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39 #else
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40 --five-prim-primer $sequencer_type.five_prim_primer --three-prim-primer $sequencer_type.three_prim_primer
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41 #end if
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42
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43 #if $sequencer_type.input_type.input_type_selected == "archive"
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44 --input-archive $sequencer_type.input_type.archive_file
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45 #if $sequencer_type.sequencer_selected == "illumina" and $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged"
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46 --already-contiged
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47 #elif $sequencer_type.sequencer_selected == "illumina"
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48 --R1-size $sequencer_type.input_type.archive_type.R1_size --R2-size $sequencer_type.input_type.archive_type.R2_size
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49 --mismatch-rate $sequencer_type.input_type.archive_type.mm_rate
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50 --merge-software $sequencer_type.input_type.archive_type.merge_software_type.merge_software_selected
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51 #if $sequencer_type.input_type.archive_type.merge_software_type.merge_software_selected == "flash"
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52 --expected-amplicon-size $sequencer_type.input_type.archive_type.merge_software_type.expected_amplicon_size
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53 #end if
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54 #if $sequencer_type.input_type.archive_type.keep_unmerged
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55 --keep-unmerged
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56 #end if
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57 #end if
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58 #else
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59 #set $sep = ' '
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60 #if $sequencer_type.sequencer_selected == "illumina"
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61 --samples-names
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62 #for $current in $sequencer_type.input_type.files_by_samples_type.samples
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63 $sep"${current.name.strip()}"
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64 #end for
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65 --input-R1
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66 #for $current in $sequencer_type.input_type.files_by_samples_type.samples
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67 $sep${current.R1_file}
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68 #end for
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69 #if $sequencer_type.input_type.files_by_samples_type.files_by_samples_type_selected == "already_merged"
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70 --already-contiged
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71 #else
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72 --input-R2
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73 #for $current in $sequencer_type.input_type.files_by_samples_type.samples
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74 $sep${current.R2_file}
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75 #end for
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76 --R1-size $sequencer_type.input_type.files_by_samples_type.R1_size --R2-size $sequencer_type.input_type.files_by_samples_type.R2_size
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77 --mismatch-rate $sequencer_type.input_type.files_by_samples_type.mm_rate
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78 --merge-software $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software_selected
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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79 #if $sequencer_type.input_type.files_by_samples_type.merge_software_type.merge_software_selected == "flash"
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80 --expected-amplicon-size $sequencer_type.input_type.files_by_samples_type.expected_amplicon_size
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81 #end if
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82 #if $sequencer_type.input_type.files_by_samples_type.keep_unmerged
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83 --keep-unmerged
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84 #end if
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85 #end if
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86 #else
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87 --input-R1
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88 #for $current in $sequencer_type.input_type.samples
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89 $sep${current.R1_file}
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90 #end for
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91 --samples-names
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92 #for $current in $sequencer_type.input_type.samples
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93 $sep"${current.name.strip()}"
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94 #end for
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95 #end if
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96 #end if
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97 </command>
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98 <inputs>
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99 <conditional name="sequencer_type">
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100 <param name="sequencer_selected" type="select" label="Sequencer" help="Select the sequencing technology used to produce the sequences.">
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101 <option value="illumina" selected="true">Illumina</option>
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102 <option value="454">454</option>
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103 </param>
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104 <when value="illumina">
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105 <!-- Samples -->
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106 <conditional name="input_type">
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107 <param name="input_type_selected" type="select" label="Input type" help="Samples files can be provided in single archive or with two files (R1 and R2) by sample.">
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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108 <option value="files_by_samples" selected="true">Files by samples</option>
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109 <option value="archive">Archive</option>
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110 </param>
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111 <when value="archive">
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112 <param name="archive_file" type="data" format="tar" label="Archive file" help="The tar file containing the sequences file(s) for each sample." optional="false" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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113 <conditional name="archive_type">
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114 <param name="archive_type_selected" type="select" label="Reads already merged ?" help="The archive contains 1 file by sample : R1 and R2 are already merged by pair.">
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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115 <option value="paired" selected="true">No</option>
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116 <option value="already_merged">Yes</option>
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117 </param>
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118 <!-- $sequencer_type.input_type.archive_type.archive_type_selected == "already_merged" -->
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119 <when value="paired">
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120 <!-- Reads size -->
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121 <param name="R1_size" type="integer" label="Reads 1 size" help="The maximum read1 size." value="" optional="false" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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122 <param name="R2_size" type="integer" label="Reads 2 size" help="The maximum read2 size." value="" optional="false" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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123 <param name="mm_rate" type="float" label="mismatch rate." help="The maximum rate of mismatch in the overlap region" value="0.1" optional="false" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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124
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125 <conditional name="merge_software_type">
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126 <param name="merge_software_selected" type="select" label="Merge software" help="Select the software to merge paired-end reads.">
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127 <option value="vsearch" selected="true">Vsearch</option>
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128 <option value="flash">Flash</option>
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129 </param>
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130 <when value="flash">
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131 <param name="expected_amplicon_size" type="integer" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons." value="" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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132 </when>
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133 <when value="vsearch"></when>
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134 </conditional>
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135 <param name="keep_unmerged" type="boolean" label="Would you like to keep unmerged reads?" help="No : Unmerged reads will be excluded; Yes : unmerged reads will be artificially combined with 100 N. (default No)" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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136 </when>
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137 <when value="already_merged"></when>
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138 </conditional>
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139 </when>
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140 <when value="files_by_samples">
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141 <conditional name="files_by_samples_type">
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142 <param name="files_by_samples_type_selected" type="select" label="Reads already contiged ?" help="The inputs contain 1 file by sample : R1 and R2 are already merged by pair.">
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143 <option value="paired" selected="true">No</option>
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144 <option value="already_merged">Yes</option>
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145 </param>
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146 <when value="paired">
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147 <!-- Samples -->
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148 <repeat name="samples" title="Samples" min="1">
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149 <param name="name" type="text" label="Name" help="The sample name." optional="false">
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150 <validator type="empty_field" message="This parameter is required." />
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151 </param>
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152 <param format="fastq" name="R1_file" type="data" label="Reads 1" help="R1 FASTQ file of paired-end reads." />
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153 <param format="fastq" name="R2_file" type="data" label="reads 2" help="R2 FASTQ file of paired-end reads." />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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154 </repeat>
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155 <!-- Reads size -->
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156 <param name="R1_size" type="integer" label="Reads 1 size" help="The maximum read1 size." value="" optional="false" />
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157 <param name="R2_size" type="integer" label="Reads 2 size" help="The maximum read2 size." value="" optional="false" />
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158 <param name="mm_rate" type="float" label="mismatch rate." help="The maximum rate of mismatches in the overlap region" value="0.1" optional="false" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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159 <conditional name="merge_software_type">
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160 <param name="merge_software_selected" type="select" label="Merge software" help="Select the software to merge paired-end reads.">
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161 <option value="vsearch" selected="true">Vsearch</option>
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162 <option value="flash">Flash</option>
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163 </param>
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164 <when value="flash">
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165 <param name="expected_amplicon_size" type="integer" label="Expected amplicon size" help="Maximum amplicon length expected in approximately 90% of the amplicons." value="" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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166 </when>
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167 <when value="vsearch"></when>
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168 </conditional>
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169 <param name="keep_unmerged" type="boolean" label="Would you like to keep unmerged reads?" help="No : Unmerged reads will be excluded; Yes : unmerged reads will be artificially combined with 100 N. (default No)" />
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170 </when>
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171 <when value="already_merged">
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172 <repeat name="samples" title="Samples" min="1">
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173 <param name="name" type="text" label="Name" help="The sample name." optional="false">
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174 <validator type="empty_field" message="This parameter is required." />
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175 </param>
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176 <param format="fastq" name="R1_file" type="data" label="Sequence file" help="FASTQ file of merged reads." />
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177 </repeat>
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178 </when>
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179 </conditional>
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180 </when>
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181 </conditional>
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182 <!-- Amplicons -->
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183 <param name="min_amplicon_size" type="integer" label="Minimum amplicon size" help="The minimum size for the amplicons (with primers)." value="" optional="false" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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184 <param name="max_amplicon_size" type="integer" label="Maximum amplicon size" help="The maximum size for the amplicons (with primers)." value="" optional="false" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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185 <!-- Primers -->
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186 <conditional name="sequencing_protocol">
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187 <param name="sequencing_protocol_selected" type="select" label="Sequencing protocol" help="The protocol used for sequencing step: standard or custom with PCR primers as sequencing primers.">
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188 <option value="standard" selected="true">Illumina standard</option>
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189 <option value="without_primers">Custom protocol (Kozich et al. 2013)</option>
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190 </param>
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191 <when value="standard">
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192 <param name="five_prim_primer" type="text" size="20" label="5' primer" help="The 5' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters'." optional="false">
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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193 <validator type="empty_field" message="This parameter is required." />
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194 </param>
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195 <param name="three_prim_primer" type="text" size="20" label="3' primer" help="The 3' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters'." optional="false">
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196 <validator type="empty_field" message="This parameter is required." />
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197 </param>
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198 </when>
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199 <when value="without_primers"></when>
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200 </conditional>
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201 </when>
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202
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203 <when value="454">
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204 <!-- Samples -->
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205 <conditional name="input_type">
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206 <param name="input_type_selected" type="select" label="Input type" help="Samples files can be provided in single archive or with one file by sample.">
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207 <option value="files_by_samples" selected="true">One file by sample</option>
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208 <option value="archive">Archive</option>
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209 </param>
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210 <when value="archive">
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211 <param name="archive_file" type="data" format="tar" label="Archive file" help="The tar file containing the sequences file for each sample." optional="false" />
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212 </when>
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213 <when value="files_by_samples">
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214 <repeat name="samples" title="Samples" min="1">
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215 <param name="name" type="text" label="Name" help="The sample name." optional="false" />
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216 <param format="fastq" name="R1_file" type="data" label="Sequence file" help="FASTQ file of sample." />
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217 </repeat>
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218 </when>
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219 </conditional>
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220 <!-- Amplicons -->
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221 <param name="min_amplicon_size" type="integer" label="Minimum amplicon size" help="The minimum size for the amplicons (with primers)." value="" optional="false" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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222 <param name="max_amplicon_size" type="integer" label="Maximum amplicon size" help="The maximum size for the amplicons (with primers)." value="" optional="false" />
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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223 <!-- Primers -->
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224 <param name="five_prim_primer" type="text" size="20" label="5' primer" help="The 5' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters'." optional="false">
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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225 <validator type="empty_field" message="This parameter is required." />
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226 </param>
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227 <param name="three_prim_primer" type="text" size="20" label="3' primer" help="The 3' primer sequence (wildcards are accepted). The orientation is detailed below in 'Primers parameters'." optional="false">
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228 <validator type="empty_field" message="This parameter is required." />
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229 </param>
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230 </when>
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231 </conditional>
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232 </inputs>
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233 <outputs>
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234 <data format="fasta" name="dereplicated_file" label="${tool.name}: dereplicated.fasta" from_work_dir="dereplicated.fasta" />
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235 <data format="tabular" name="count_file" label="${tool.name}: count.tsv" from_work_dir="count.tsv" />
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236 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html" />
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237 </outputs>
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238 <tests>
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239 <test>
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240 <conditional name="sequencer_type">
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241 <param name="sequencer_selected" value="illumina"/>
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242 <conditional name="input_type">
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243 <param name="input_type_selected" value="archive"/>
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244 <param name="archive_file" ftype="tar" value="input/test_dataset.tar.gz"/>
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245 <conditional name="archive_type">
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246 <param name="archive_type_selected" value="paired"/>
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247 <param name="R1_size" value="267"/>
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248 <param name="R2_size" value="266"/>
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249 <param name="mm_rate" value="0.15"/>
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250 <conditional name="merge_software_type">
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251 <param name="merge_software_selected" value="flash" />
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252 <param name="expected_amplicon_size" value="420"/>
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253 </conditional>
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254 <param name="keep_unmerged" value="true"/>
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255 </conditional>
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256 </conditional>
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257 <param name="min_amplicon_size" value="44"/>
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258 <param name="max_amplicon_size" value="490"/>
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259 <conditional name="sequencing_protocol">
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260 <param name="sequencing_protocol_selected" value="standard"/>
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261 <param name="five_prim_primer" value="GGCGVACGGGTGAGTAA"/>
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262 <param name="three_prim_primer" value="GTGCCAGCNGCNGCGG"/>
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263 </conditional>
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264 </conditional>
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265 <output name="dereplicated_file" file="references/01-prepro-flash.fasta"/>
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266 <output name="count_file" file="references/01-prepro-flash.tsv"/>
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267 <output name="summary_file" file="references/01-prepro-flash.html" compare="sim_size" delta="0"/>
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268 <!--output name="summary_file">
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269 <assert_contents>
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270 <has_text_matching expression="FROGS\sPre-process" />
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271 <has_text_matching expression="splA_01" />
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272 </assert_contents>
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273 </output-->
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274 </test>
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275 <test>
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276 <conditional name="sequencer_type">
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277 <param name="sequencer_selected" value="illumina"/>
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278 <conditional name="input_type">
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279 <param name="input_type_selected" value="archive"/>
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280 <param name="archive_file" ftype="tar" value="input/test_dataset.tar.gz"/>
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281 <conditional name="archive_type">
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282 <param name="archive_type_selected" value="paired"/>
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283 <param name="R1_size" value="267"/>
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284 <param name="R2_size" value="266"/>
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285 <param name="mm_rate" value="0.15"/>
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286 <conditional name="merge_software_type">
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287 <param name="merge_software_selected" value="vsearch" />
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288 </conditional>
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289 <param name="keep_unmerged" value="true"/>
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290 </conditional>
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291 </conditional>
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292 <param name="min_amplicon_size" value="44"/>
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293 <param name="max_amplicon_size" value="490"/>
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294 <conditional name="sequencing_protocol">
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295 <param name="sequencing_protocol_selected" value="standard"/>
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296 <param name="five_prim_primer" value="GGCGVACGGGTGAGTAA"/>
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297 <param name="three_prim_primer" value="GTGCCAGCNGCNGCGG"/>
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298 </conditional>
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299 </conditional>
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300 <output name="dereplicated_file" file="references/01-prepro-vsearch.fasta"/>
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301 <output name="count_file" file="references/01-prepro-vsearch.tsv"/>
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302 <output name="summary_file" file="references/01-prepro-vsearch.html" compare="sim_size" delta="0"/>
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303 <!--output name="summary_file">
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304 <assert_contents>
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305 <has_text_matching expression="FROGS\sPre-process" />
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306 <has_text_matching expression="splA_01" />
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307 </assert_contents>
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308 </output-->
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309 </test>
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310 </tests>
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311 <help>
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312
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313 .. image:: static/images/frogs_images/FROGS_logo.png
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314 :height: 144
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315 :width: 110
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316
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317
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318 .. class:: infomark page-header h2
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319
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320 What it does
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321
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322 FROGS Pre-process filters and dereplicates amplicons for use in diversity analysis.
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323
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324 .. class:: infomark page-header h2
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325
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326 Inputs/Outputs
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327
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328 .. class:: h3
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329
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330 Inputs
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331
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332 Sample files added one after another or provide in an archive file (tar.gz).
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333
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334 .. container:: row
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335
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336 .. container:: col-md-6
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337
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338 **Illumina inputs**
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339
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340 :Usage: For samples sequenced in paired-end. The amplicon length must be inferior to the length of the R1 plus R2 length. R1 and R2 are merged by the common region.
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341 :Files: One R1 and R2 by sample (format `FASTQ &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_)
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342 :Example: splA_R1.fastq.gz, splA_R2.fastq.gz, splB_R1.fastq.gz, splB_R2.fastq.gz
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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343
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344 OR
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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345
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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346 :Usage: For samples sequenced in single-ends or when R1 and R2 reads are already merged.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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347 :Files: One sequence file by sample (format `FASTQ &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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348 :Example: splA.fastq.gz, splB.fastq.gz
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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349
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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350 .. container:: col-md-6
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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351
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352 **454 inputs**
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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353
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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354 :Files: One sequence file by sample (format `FASTQ &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_)
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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355 :Example: splA.fastq.gz, splB.fastq.gz
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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356
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357 Remark: In an archive if you use R1 and R2 files they names must end with *_R1* and *_R2*.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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358
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359 .. class:: h3
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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360
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361 Outputs
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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362
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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363 **Sequence file** (dereplicated.fasta):
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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364
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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365 Only one file with all samples sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_). These sequences are dereplicated: strictly identical sequence are represented only once and the initial count is kept in count file.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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366
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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367 **Count file** (count.tsv):
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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368
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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369 This file contains the count of all unique sequences in each sample (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_).
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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370
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371 **Summary file** (report.html):
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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372
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373 This file reports the number of remaining sequences after each filter (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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374
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375 .. image:: static/images/frogs_images/FROGS_preprocess_summary_v3.png
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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376 :height: 850
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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377 :width: 831
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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378
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379 It also presents the length distribution of the remaining full amplicon sequences.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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380
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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381 .. image:: static/images/frogs_images/FROGS_preprocess_lengthsSamples_v3.png
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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382 :height: 379
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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383 :width: 364
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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384
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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385 .. class:: infomark page-header h2
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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386
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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387 How it works
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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388
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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389 .. csv-table::
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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390 :header: "Steps", "Illumina", "454"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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391 :widths: 5, 150, 150
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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392 :class: table table-striped
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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393
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394 "1", "For un-merged data: merges R1 and R2 with a maximum of M% mismatch in the overlaped region(`VSEARCH &lt;https://github.com/torognes/vsearch/&gt;`_ or `FLASH &lt;https://ccb.jhu.edu/software/FLASH/&gt;`_ or optionnaly `PEAR &lt;https://sco.h-its.org/exelixis/web/software/pear/&gt;`_). Resulting un-merged reads may optionnaly be artificially combined by adding 100 N between the reads", "/"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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395 "2", "If sequencing protocol is the illumina standard protocol : Removes sequences where the two primers are not present and then remove primers in the remaining sequence (`cutadapt &lt;http://cutadapt.readthedocs.org/en/latest/guide.html&gt;`_). The primer search accepts 10% of differences", "Removes sequences where the two primers are not present, removes primers sequence and reverse complement the sequences on strand - (`cutadapt &lt;http://cutadapt.readthedocs.org/en/latest/guide.html&gt;`_). The primer search accepts 10% of differences"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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396 "3", "Filters sequences with ambiguous nucleotides and for merged sequences filters on their length which must be range between 'Minimum amplicon size - primer length' and 'Maximum amplicon size - primer length'", "the tool removes sequences with at least one homopolymer with more than seven nucleotides and with a distance of less than or equal to 10 nucleo-tides between two poor quality positions, i.e. with a Phred quality score lesser than 10"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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397 "4", "Dereplicates sequences", "Dereplicates sequences"
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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398
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399
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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400 .. class:: infomark page-header h2
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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401
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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402 Advices/details on parameters
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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403
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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404 .. class:: h3
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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405
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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406 What is the differency between overlapped sequences and combined sequences?
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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407
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408 - **Case of a sequencing of overlapping sequences: case of 16S V3-V4 amplicon MiSeq sequencing**
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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409
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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410 .. image:: static/images/frogs_images/FROGS_preprocess_overlapped_sequence.png
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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411 :height: 261
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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412 :width: 531
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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413
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414 - **Case of a sequencing of non-overlapping sequences: case of ITS1 amplicon MiSeq sequencing**
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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415
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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416 .. image:: static/images/frogs_images/FROGS_preprocess_combined_sequence1.png
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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417 :height: 279
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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418 :width: 797
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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419
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420 .. class:: warningmark
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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421
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422 **“FROGS combined” warning points**
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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423
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424 Reads pair are not merged because:
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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425
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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426 - the real amplicon length is greater than de number of base sequences (500 bp for MiSeq 2x250bp)
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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427 - the overlapped region is smaller than 10 (fixed parameter in FROGS).
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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428
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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429 Thus, “FROGS combined” sequences are artificial and present particular features especially on size.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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430 Imagine a MiSeq sequencing of 2x250pb with sequences that cannot overlap, the resulting “FROGS combined” sequences length will be 600 bp.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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431
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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432 .. image:: static/images/frogs_images/FROGS_preprocess_combined_sequence2.png
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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433 :height: 357
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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434 :width: 798
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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435
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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436 .. class:: h3
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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437
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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438 Keeping or not un-merged paired reads
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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439
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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440 This option is usefull when and only when, targeted amplicon is longer than the sequencing technology can provide (ITS amplicon for example). In other case, carefully, you will only keep noise in your analysis.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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441
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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442
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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443 .. class:: h3
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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444
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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445 Primers parameters
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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446
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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447 The (`Kozich et al. 2013 &lt;http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/&gt;`_ ) protocol uses custom sequencing primers which are also the PCR primers. In this case the reads do not contain the PCR primers.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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448
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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449 In case of Illumina standard protocol, the primers must be provided in 5' to 3' orientation.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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450
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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451 .. role:: alert-info
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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452
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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453 Example:
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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454
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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455 5' :alert-info:`ATGCCC` GTCGTCGTAAAATGC :alert-info:`ATTTCAG` 3'
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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456
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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457 Value for parameter 5' primer: ATGCCC
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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458
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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459 Value for parameter 3' primer: ATTTCAG
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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460
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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461 .. class:: h3
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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462
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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463 FLASH : Amplicons sizes parameters
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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464
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465 The two following images show two examples of perfect values fors sizes parameters.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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466
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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467 .. image:: static/images/frogs_images/FROGS_preprocess_ampliconSize_unimodal_v3.png
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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468 :height: 415
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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469 :width: 676
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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470
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471 .. image:: static/images/frogs_images/FROGS_preprocess_ampliconSize_multimodal_v3.png
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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472 :height: 415
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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473 :width: 676
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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474
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475 Don't worry the "Expected amplicon size" does not need to be very accurate, and only necessary for sequences merging with FLASH.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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476
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477 .. class:: h3
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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478
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479 If the filter 'merged' reduce drasticaly the number of sequences:
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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480
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481 In un-merged Illumina data, the reduction of dataset by the merged filter is classicaly inferior than 20%. A loss of more than 20% in all samples can highlight a quality problem.
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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482
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483 If the overlap between R1 and R2 is superior to 50 nucleotides and the quality of the end of the sequences is poor (see `FastQC &lt;http://www.bioinformatics.babraham.ac.uk/projects/fastqc/&gt;`_) you can try to cut the end of your sequences and relaunch the preprocess tool. You can either raise the mismatch percent in the overlapped region, but not too much!
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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484
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485 ----
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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486
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487 **Contact**
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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488
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489 Contacts: frogs@inra.fr
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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490
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491 Repository: https://github.com/geraldinepascal/FROGS
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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492 website: http://frogs.toulouse.inra.fr/
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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493
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494 Please cite the **FROGS article**: *Escudie F., et al. Bioinformatics, 2018. FROGS: Find, Rapidly, OTUs with Galaxy Solution.*
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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495
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496 </help>
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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497 <citations>
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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498 <citation type="doi">10.1093/bioinformatics/btx791</citation>
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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499 </citations>
59bc96331073 planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/tree/v3.1.0 commit 08296fc88e3e938c482c631bd515b3b7a0499647
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500
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501 </tool>