annotate remove_chimera.xml @ 0:76c750c5f0d1 draft default tip

planemo upload for repository https://github.com/oinizan/FROGS-wrappers commit 0b900a51e220ce6f17c1e76292c06a5f4d934055-dirty
author frogs
date Thu, 25 Oct 2018 05:01:13 -0400
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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_remove_chimera" name="FROGS Remove chimera" version="1.3.0">
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19 <description>Step 3 in metagenomics analysis : Remove PCR chimera in each sample.</description>
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20 <requirements>
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21 <requirement type="package" version="2.0.1">frogs</requirement>
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22 </requirements>
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23 <stdio>
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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 remove_chimera.py
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29 --nb-cpus $nb_cpus
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30 --input-fasta $sequence_file --non-chimera $non_chimera_fasta
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31 --summary $summary_file
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32 #if $abundance_type.abundance_type_selected == "biom"
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33 --input-biom $abundance_biom
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34 --out-abundance $out_abundance_biom
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35 #else
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36 --input-count $abundance_count
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37 --out-abundance $out_abundance_count
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38 #end if
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39 </command>
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40 <inputs>
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41 <!-- Files -->
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42 <param format="fasta" name="sequence_file" type="data" label="Sequences file" help="The sequences file (format: fasta)." optional="false" />
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43 <conditional name="abundance_type">
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44 <param name="abundance_type_selected" type="select" label="Abundance type" help="Select the type of file where the abundance of each sequence by sample is stored.">
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45 <option value="biom" selected="true">BIOM file</option>
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46 <option value="count">TSV file</option>
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47 </param>
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48 <when value="biom">
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49 <param format="biom1" name="abundance_biom" type="data" label="Abundance file" help="It contains the count by sample for each sequence." optional="false" />
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50 </when>
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51 <when value="count">
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52 <param format="tabular" name="abundance_count" type="data" label="Count file" help="It contains the count by sample for each sequence (see below)." optional="false" />
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53 </when>
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54 </conditional>
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55 <!-- Parameters -->
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56 <param name="nb_cpus" type="hidden" label="CPU number" help="The maximum number of CPUs used." value="1" />
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57 <!--
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58 <param name="size_separator" type="text" label="Size separator" help="Fill this input only if the IDs of sequences in fasta store the abundance as suffix. Example: 'Cluster_1;size=10' => ';size='" value="" optional="true" />
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59 -->
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60 </inputs>
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61 <outputs>
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62 <data format="fasta" name="non_chimera_fasta" label="${tool.name}: non_chimera.fasta" from_work_dir="non_chimera.fasta"/>
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63 <data format="biom1" name="out_abundance_biom" label="${tool.name}: non_chimera_abundance.biom" from_work_dir="non_chimera_abundance.biom">
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64 <filter>abundance_type['abundance_type_selected'] == "biom"</filter>
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65 </data>
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66 <data format="tabular" name="out_abundance_count" label="${tool.name}: non_chimera_abundance.tsv" from_work_dir="non_chimera_abundance.tsv">
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67 <filter>abundance_type['abundance_type_selected'] == "count"</filter>
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68 </data>
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69 <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/>
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="sequence_file" value="references/02-clustering.fasta"/>
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74 <conditional name="abundance_type">
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75 <param name="abundance_type_selected" value="biom"/>
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76 <param name="abundance_biom" value="references/02-clustering.biom" />
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77 </conditional>
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78 <output name="non_chimera_fasta" file="references/03-chimera.fasta"/>
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79 </test>
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80 </tests>
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81 <help>
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82
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83 .. image:: static/images/FROGS_logo.png
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84 :height: 144
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85 :width: 110
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86
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87
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88 .. class:: infomark page-header h2
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89
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90 What it does
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91
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92 Remove chimeric sequences by sample.
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93
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94
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95 .. class:: infomark page-header h2
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96
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97 Context
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98
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99 Chimeras are sequences formed from two or more biological sequences joined together.
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100
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101 The majority of these anomalous sequences are formed from an incomplete extension during a PCR cycle. During subsequent cycles, a partially extended strand can bind to a template derived from a different but similar sequence.
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102
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103 This phenomena is particularly common in amplicon sequencing where closely related sequences are amplified.
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104
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105
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106 .. class:: infomark page-header h2
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107
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108 Inputs/Outputs
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109
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110 .. class:: h3
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111
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112 Inputs
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113
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114 **Sequence file**:
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115
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116 The sequences (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
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117
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118 **Abundance file**:
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119
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120 The abundance of each cluster in each sample (format `BIOM &lt;http://biom-format.org/&gt;`_).
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121
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122 OR
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123
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124 The abundance of each sequence in each sample (format `TSV &lt;https://en.wikipedia.org/wiki/Tab-separated_values&gt;`_). This type of file is produced by *FROGS pre-process*.
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125
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126 Example::
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127
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128 #id splA splB
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129 seq1 1289 2901
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130 seq2 3415 0
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131
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132 .. class:: h3
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133
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134 Outputs
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135
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136 **Sequence file** (non_chimera.fasta):
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137
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138 The sequence file with only non-chimera (format `FASTA &lt;https://en.wikipedia.org/wiki/FASTA_format&gt;`_).
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139
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140 **Abundance file** (non_chimera.biom or non_chimera.tsv):
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141
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142 The abundance file with only non-chimera (format the same of the abundance input).
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143
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144 **Summary file** (report.html):
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145
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146 This file presents the number of removed elements (format `HTML &lt;https://en.wikipedia.org/wiki/HTML&gt;`_).
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147
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148
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149 .. class:: infomark page-header h2
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150
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151 How it works
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152
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153 .. csv-table::
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154 :header: "Steps", "Description"
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155 :widths: 10, 90
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156 :class: table table-striped
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157
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158 "1", "Split input data by sample (classicaly the PCR is realised by sample)."
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159 "2", "Find chimera in each sample (`vsearch &lt;https://github.com/torognes/vsearch&gt;`_)."
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160 "3", "Remove the sequences identify as chimera in all samples where they are present."
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161
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162
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163 ----
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164
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165 **Contact**
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166
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167 Contacts: frogs@inra.fr
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168
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169 Repository: https://github.com/geraldinepascal/FROGS
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170
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171 Please cite the FROGS Publication: *Escudie F., Auer L., Bernard M., Cauquil L., Vidal K., Maman S., Mariadassou M., Hernadez-Raquet G., Pascal G., 2015. FROGS: Find Rapidly OTU with Galaxy Solution. In: The environmental genomic Conference, Montpellier, France,* http://bioinfo.genotoul.fr/fileadmin/user_upload/FROGS_2015_GE_Montpellier_poster.pdf
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172
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173 Depending on the help provided you can cite us in acknowledgements, references or both.
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174 </help>
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175 <citations>
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176 <citation type="doi">10.7287/peerj.preprints.386v1</citation>
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177 </citations>
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178 </tool>