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annotate binette.xml @ 0:8faabc0f7f46 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binette/ commit 59b031eff1c156122720281e42b0eaa8d3724c57
author iuc
date Mon, 20 Jan 2025 16:19:23 +0000
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children 6108dc80d9b2
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8faabc0f7f46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binette/ commit 59b031eff1c156122720281e42b0eaa8d3724c57
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1 <tool id="binette" name="Binette" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Binning refinement tool</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.5</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <token name="@PROFILE@">24.1</token>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">binette</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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13 mkdir -p 'input' 'output' &&
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14
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15 #for $i, $file in enumerate($contig2bin_tables):
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16 ln -s '$file' 'input/bin_table_${i}.tsv' &&
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17 #end for
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19 ln -s '$contigs' 'input_contigs.fasta' &&
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20 #if $database_type.is_select == 'his':
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21 ln -s '$checkm2_db' 'input_database.dmnd' &&
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22 #end if
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24 #if $proteins:
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25 ln -s '$proteins' 'input_proteins.fasta' &&
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26 #end if
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27
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28 binette
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29 -b input/*.tsv
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30 -c 'input_contigs.fasta'
8faabc0f7f46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/binette/ commit 59b031eff1c156122720281e42b0eaa8d3724c57
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31 #if $proteins:
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32 -p 'input_proteins.fasta'
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33 #end if
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34 -m ${min_completeness}
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35 -t "\${GALAXY_SLOTS:-1}"
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36 -o 'output/'
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37 -w ${contamination_weight}
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38 #if $database_type.is_select == 'his':
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39 --checkm2_db 'input_database.dmnd'
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40 #else
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41 --checkm2_db '$datamanager.fields.path'
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42 #end if
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43
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44 ]]>
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45 </command>
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46 <inputs>
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47 <param argument="--contig2bin_tables" type="data" multiple="true" min="2" format="tabular" label="Input contig table"
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48 help="Input at least 2 different contig tables. Look into the help section at the bottom for more information!"/>
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49 <param argument="--contigs" type="data" format="fasta,fasta.gz" label="Input contig file"/>
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50 <param argument="--proteins" type="data" format="fasta,fasta.gz" optional="true" label="Input FASTA file in Prodigal format (>contigID_geneID)"
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51 help="If this file is provided all predicted genes contained in this file will be skipped. A example for this format is in the help section"/>
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52 <param argument="--min_completeness" type="integer" min="0" max="100" value="40" label="Set minimus completeness"
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53 help="Threshold for bins for the final bin selection"/>
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54 <param argument="--contamination_weight" type="integer" value="2" label="Set contamination weight"
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55 help="This weight is used for the scoring the bins. A low weight favor complete bins over low contaminated bins"/>
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56 <conditional name="database_type">
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57 <param name="is_select" type="select" label="Select if database should be used either via file or cached database">
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58 <option value="cached">cached database</option>
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59 <option value="his">History</option>
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60 </param>
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61 <when value="his">
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62 <param argument="--checkm2_db" type="data" format="dmnd" label="Input CheckM2 diamond database"
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63 help="When a CheckM2 diamond database should be used download and input it here."/>
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64 </when>
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65 <when value="cached">
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66 <param name="datamanager" type="select" label="Select reference genome" help="Checkm2 Diamond database">
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67 <options from_data_table="checkm2">
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68 <filter type="sort_by" column="2"/>
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69 </options>
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70 <validator type="no_options" message="No databases are available for this version of Checkm2. Please contact the Galaxy administrators to request one be installed."/>
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71 </param>
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72 </when>
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73 </conditional>
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74 </inputs>
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75 <outputs>
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76 <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
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77 <discover_datasets pattern="((?P&lt;designation&gt;.*)\.fa)" format="fasta" directory="output/final_bins"/>
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78 </collection>
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79 <collection name="quality" type="list" label="${tool.name} on ${on_string}: Quality Report">
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80 <discover_datasets pattern="((?P&lt;designation&gt;.*)\.tsv)" format="tabular" directory="output/input_bins_quality_reports"/>
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81 </collection>
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82 <data name="final" format="tabular" from_work_dir="output/final_bins_quality_reports.tsv" label="${tool.name} on ${on_string}: Final Quality Report"/>
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83 </outputs>
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84 <tests>
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85 <test expect_num_outputs="3">
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86 <param name="contig2bin_tables" ftype="tabular" value="A.binning,B.binning,C.binning"/>
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87 <param name="contigs" value="all_contig.fasta.gz" ftype="fasta.gz"/>
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88 <param name="min_completeness" value="5"/>
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89 <param name="contamination_weight" value="0"/>
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90 <conditional name="database_type">
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91 <param name="is_select" value="his"/>
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92 <param name="checkm2_db" value="checkm2_tiny_db.dmnd"/>
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93 </conditional>
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94 <output name="final" ftype="tabular">
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95 <assert_contents>
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96 <has_text text="binC"/>
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97 <has_text text="50"/>
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98 <has_text text="9"/>
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99 </assert_contents>
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100 </output>
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101 <output_collection name="bins" count="4"/>
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102 </test>
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103 <test expect_num_outputs="3">
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104 <param name="contig2bin_tables" ftype="tabular" value="A.binning,B.binning,C.binning"/>
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105 <param name="contigs" value="all_contig.fasta.gz" ftype="fasta.gz"/>
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106 <param name="min_completeness" value="40"/>
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107 <param name="contamination_weight" value="2"/>
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108 <conditional name="database_type">
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109 <param name="is_select" value="cached"/>
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110 <param name="datamanager" value="test_db"/>
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111 </conditional>
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112 <param name="proteins" ftype="fasta.gz" value="proteins.fasta.gz"/>
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113 <output name="final" ftype="tabular">
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114 <assert_contents>
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115 <has_text text="binC"/>
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116 <has_text text="50"/>
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117 <has_text text="40"/>
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118 </assert_contents>
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119 </output>
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120 <output_collection name="bins" count="4"/>
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121 </test>
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122 </tests>
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123 <help>
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124 <![CDATA[
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125
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126 .. class:: infomark
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127
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128 **What does Binette**
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129
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130 Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools.
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131
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132 **Inputs**
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133
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134 - At least 2 different contig tables.
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135
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136 .. class:: infomark
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137
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138 The contig tables can be generate by the tool *Converts genome bins in fasta format*. This tool only need the bins which where created by any binner as input.
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139
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140 - The contig file
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141
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142 .. class:: infomark
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143
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144 This file should contain all reads used to create the bins. The format of this file should be either fasta or fasta.gz.
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145
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146 - A CheckM2 diamond database
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147
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148 .. class::infomark
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149
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150 This database can be download with using the CheckM2 package and the followed command: *checkm2 database --download --path <checkm2/database/>* or it is possible to use a database cached on Galaxy.
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151
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152
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153 - An optional (fasta/fasta.gz) file with predicted genes
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154
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155 .. class:: infomark
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156
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157 This file, in a fasta format, is generate with the tool *Prodigal*
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158
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159 Example:
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160
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161 ::
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162
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163 >Chlamydia_trachomatis_part1_1 # 1 # 1776 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.466
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164 MSIRGVGGNGNSRIPSHNGDGSNRRSQNTKGNNKVEDRVCSLYSSRSNENRESPYAVVDV
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165 SSMIESTPTSGETTRASRGVFSRFQRGLVRIADKVRRAVQCAWSSVSTSRSSATRAAESG
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166 SSSRTARGASSGYREYSPSAARGLRLMFTDFWRTRVLRQTSPMAGVFGNLDVNEARLMAA
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167 YTSECADHLEAKELAGPDGVAAAREIAKRWEKRVRDLQDKGAARKLLNDPLGRRTPNYQS
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168 KNPGEYTVGNSMFYDGPQVANLQNVDTGFWLDMSNLSDVVLSREIQTGLRARATLEESMP
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169 MLENLEERFRRLQETCDAARTEIEESGWTRESASRMEGDEAQGPSRAQQAFQSFVNECNS
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170 IEFSFGSFGEHVRVLCARVSRGLAAAGEAIRRCFSCCKGSTHRYAPRDDLSPEGASLAET
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171 LARFADDMGIERGADGTYDIPLVDDWRRGVPSIEGEGSDSIYEIMMPIYEVMNMDLETRR
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172 SFAVQQGHYQDPRASDYDLPRASDYDLPRSPYPTPPLPPRYQLQNMDVEAGFREAVYASF
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173 VAGMYNYVVTQPQERIPNSQQVEGILRDMLTNGSQTFRDLMKRWNREVDRE*
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174
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175 **Outputs**
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176
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177 - A collection (list) with all the selected bins in fasta format.
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178
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179 - A final quality report file containing quality information about the final selected bins.
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180
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181 - A collection (list) storing quality reports for the input bin sets, with files following the same structure as the final quality report file.
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182
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183 ]]>
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184 </help>
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185 <citations>
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186 <citation type="doi">10.21105/joss.06782</citation>
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187 </citations>
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188 </tool>