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annotate macros.xml @ 5:ffeabd4e2c1b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit f940e776e4eba38a0a9c299c3675f59e2c1c7e7b
author iuc
date Mon, 06 Nov 2023 09:11:32 +0000
parents 965f73e77296
children 9902c85117a4
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1 <?xml version="1.0"?>
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2 <macros>
5
ffeabd4e2c1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit f940e776e4eba38a0a9c299c3675f59e2c1c7e7b
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3 <token name="@TOOL_VERSION@">3.4.5</token>
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@PROFILE@">20.01</token>
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6 <xml name="biotools">
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7 <xrefs>
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8 <xref type="bio.tools">drep</xref>
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9 </xrefs>
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10 </xml>
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11 <xml name="requirements">
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">drep</requirement>
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14 <yield/>
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15 </requirements>
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16 </xml>
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17 <xml name="citations">
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18 <citations>
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19 <citation type="doi">10.1038/ismej.2017.126</citation>
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20 <yield />
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21 </citations>
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22 </xml>
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23
1
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24 <xml name="genomes">
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25 <param argument="--genomes" type="data" format="fasta" multiple="true" label="Genomes to filer"/>
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26 </xml>
0
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27
1
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28 <!-- Addition of ".fasta" after names to avoid string to be read as integer
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29 Bug in dRep: probably fixed in next version -->
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30 <token name="@PREPARE_GENOMES@"><![CDATA[
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31 #import re
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32 #set $genomefiles = []
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33 #for $genome in $genomes
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34 #set $input_name = $re.sub('[^\w\-_.]', '_',str($genome.element_identifier.split('/')[-1]))
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35 ln -s '${genome}' '${input_name}.fasta' &&
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36 $genomefiles.append($input_name)
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37 #end for
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38 ]]></token>
0
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39 <token name="@GENOMES@"><![CDATA[
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40 -g
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41 #for $genomefile in $genomefiles
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42 '${genomefile}.fasta'
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43 #end for
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44 ]]></token>
0
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46 <xml name="filtering_options">
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47 <section name="filter" title="Genome filtering" expanded="true">
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48 <param argument="--length" type="integer" value="50000" label="Minimum genome length"/>
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49 <param argument="--completeness" type="integer" value="75" min="0" max="100" label="Minimum genome completeness percent"/>
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50 <param argument="--contamination" type="integer" value="25" min="0" max="100" label="Maximum genome contamination percent"/>
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51 </section>
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52 </xml>
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53 <xml name="test_default_filtering_options">
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54 <section name="filter">
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55 <param name="length" value="50000"/>
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56 <param name="completeness" value="75"/>
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57 <param name="contamination" value="100"/>
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58 </section>
0
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59 </xml>
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60 <token name="@FILTER_OPTIONS@"><![CDATA[
1
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61 --length $filter.length
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62 --completeness $filter.completeness
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63 --contamination $filter.contamination
0
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64 ]]></token>
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65
1
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66 <xml name="quality_assessment_options">
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67 <conditional name="quality">
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68 <param name="source" type="select" label="Genome quality filtering" help="No checkM or quality filtering is not recommened but with bacteriophages or eukaryotes or things where checkM scoring does not work. Will only choose genomes based on length and N50.">
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69 <option value="checkm" selected="true">Run checkM</option>
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70 <option value="genomeInfo">Provide quality information on the genome (CSV file)</option>
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71 <option value="ignoreGenomeQuality">Don't run checkM or do any quality filtering (--ignoreGenomeQuality) - NOT RECOMMENDED!</option>
0
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72 </param>
1
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73 <when value="checkm">
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74 <param argument="--checkM_method" type="select" label="CheckM method">
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75 <option value="lineage_wf" selected="true">lineage_wf: Lineage-specific Workflow - quality estimates with lineage-specific markers (more accurate)</option>
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76 <option value="taxonomy_wf">taxonomy_wf: Taxonomic-specific Workflow - quality estimates with taxonomic-specific markers (faster)</option>
0
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77 </param>
1
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78 <param argument="--set_recursion" type="integer" optional="true" label="Increases the python recursion limit" help="NOT RECOMMENDED unless checkM is crashing due to recursion issues. Recommended to set to 2000 if needed, but setting this could crash Python"/>
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79 <param argument="--checkm_group_size" type="integer" value="2000" min="1" label="Number of genomes passed to checkM at a time" help="Increasing this increases RAM but makes checkM faster"/>
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80 </when>
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81 <when value="genomeInfo">
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82 <param argument="--genomeInfo" type="data" format="csv" label="Quality information on the genomes">
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83 <help><![CDATA[
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84 A CSV dataset that must contain: [
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85 "genome"(history dataset name of .fasta dataset of that genome),
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86 "completeness"(0-100 value for completeness of the genome),
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87 "contamination"(0-100 value of the contamination of the genome)]
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88 ]]></help>
0
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89 </param>
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90 </when>
1
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91 <when value="ignoreGenomeQuality"/>
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92 </conditional>
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93 </xml>
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94 <xml name="test_default_quality_assessment_options">
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95 <conditional name="quality">
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96 <param name="source" value="checkm"/>
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97 <param name="checkM_method" value="taxonomy_wf"/>
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98 <param name="checkm_group_size" value="2000"/>
0
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99 </conditional>
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100 </xml>
1
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101 <token name="@QUALITY_ASSESSMENT_OPTIONS@"><![CDATA[
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102 #if $quality.source == 'checkm'
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103 --checkM_method '$quality.checkM_method'
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104 #if str($quality.set_recursion) != ''
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105 --set_recurison $filter.set_recursion
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106 #end if
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107 --checkm_group_size $quality.checkm_group_size
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108 #else if $quality.source == 'genomeInfo'
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109 --genomeInfo '$quality.genomeInfo'
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110 #else if $quality.source == 'ignoreGenomeQuality'
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111 --ignoreGenomeQuality
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112 #end if
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113 ]]></token>
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114
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115 <xml name="mash">
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116 <param argument="--MASH_sketch" type="integer" value="1000" min="0" label="MASH sketch size"/>
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117 <param argument="--P_ani" type="float" value="0.9" min="0." max="1." label="ANI threshold to form primary clusters"/>
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118 <param argument="--multiround_primary_clustering" type='boolean' checked="false" truevalue='--multiround_primary_clustering' falsevalue='' label="Cluster each primary clunk separately and merge at the end with single linkage?" help="Decreases RAM usage and increases speed, and the cost of a minor loss in precision and the inability to plot primary_clustering_dendrograms. Especially helpful when clustering 5000+ genomes. Will be done with single linkage clustering"/>
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119 <param argument="--primary_chunksize" type="integer" value="5000" min="1" label="Impacts multiround_primary_clusterings" help=" If you have more than this many genomes, process them in chunks of this size"/>
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120 </xml>
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121 <xml name="test_default_mash">
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122 <param name="MASH_sketch" value="1000"/>
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123 <param name="P_ani" value="0.9"/>
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124 <param name="multiround_primary_clustering" value=''/>
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125 <param name="primary_chunksize" value="5000"/>
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126 </xml>
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127 <token name="@MASH@"><![CDATA[
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128 --MASH_sketch '$comp_clust.steps.MASH_sketch'
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129 --P_ani $comp_clust.steps.P_ani
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130 $comp_clust.steps.multiround_primary_clustering
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131 --primary_chunksize $comp_clust.steps.primary_chunksize
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132 ]]></token>
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133
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134 <xml name="nucmer">
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135 <param argument="--n_PRESET" type="select" label="Presets to pass to nucmer">
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136 <option value="normal" selected="true">normal: default ANIn parameters</option>
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137 <option value="tight">tight: only align highly conserved regions</option>
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138 </param>
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139 </xml>
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140 <xml name="test_default_nucmer">
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141 <param name="n_PRESET" value="normal"/>
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142 </xml>
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143 <token name="@NUCMER@"><![CDATA[
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144 --n_PRESET '$comp_clust.steps.clustering.n_PRESET'
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145 ]]></token>
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146
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147 <xml name="coverage_method">
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148 <param argument="--coverage_method" type="select" label="Method to calculate coverage of an alignment">
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149 <option value="larger" selected="true">Larger = max((aligned length / genome 1), (aligned_length / genome2))</option>
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150 <option value="total">Total = 2*(aligned length) / (sum of total genome lengths)</option>
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151 </param>
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152 </xml>
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153 <xml name="test_default_coverage_method">
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154 <param name="coverage_method" value="larger"/>
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155 </xml>
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156 <token name="@COVERAGE_METHOD@"><![CDATA[
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157 --coverage_method '$comp_clust.steps.clustering.coverage_method'
0
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158 ]]></token>
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159
1
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160 <xml name="secondary_clustering">
0
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161 <conditional name="clustering">
1
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162 <param argument="--S_algorithm" type="select" label="Algorithm for secondary clustering comparisons">
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163 <option value="fastANI">fastANI: Kmer-based approach - very fast</option>
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164 <option value="ANImf" selected="true">ANImf: Align whole genomes with nucmer; filter alignment; compare aligned regions - RECOMMENDED</option>
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165 <option value="ANIn">ANIn: Align whole genomes with nucmer; compare aligned regions</option>
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166 <option value="gANI">gANI: Identify and align ORFs; compare aligned ORFS</option>
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167 <option value="goANI">Open source version of gANI; requires nsmimscan</option>
0
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168 </param>
1
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169 <when value="fastANI">
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170 <param argument="--greedy_secondary_clustering" type='boolean' checked="false" truevalue='--greedy_secondary_clustering' falsevalue='' label="Use a heuristic to avoid pair-wise comparisons when doing secondary clustering?" help="Will be done with single linkage clustering"/>
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171 </when>
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172 <when value="ANImf">
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173 <expand macro="nucmer"/>
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174 <expand macro="coverage_method"/>
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175 </when>
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176 <when value="ANIn">
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177 <expand macro="nucmer"/>
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178 <expand macro="coverage_method"/>
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179 </when>
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180 <when value="gANI"/>
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181 <when value="goANI"/>
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182 </conditional>
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183 <param argument="--S_ani" type="float" value="0.99" min="0." max="1." label="ANI threshold to form secondary clusters"/>
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184 <param argument="--cov_thresh" type="float" value="0.1" min="0." max="1." label="Minmum level of overlap between genomes when doing secondary comparisons"/>
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185 </xml>
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186 <xml name="test_default_secondary_clustering">
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187 <conditional name="clustering">
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188 <param name="S_algorithm" value="ANImf"/>
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189 <expand macro="test_default_nucmer"/>
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190 <expand macro="test_default_coverage_method"/>
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191 </conditional>
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192 <param name="S_ani" value="0.99"/>
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193 <param name="cov_thresh" value="0.1"/>
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194 </xml>
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195 <token name="@SECONDARY_CLUSTERING@"><![CDATA[
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196 --S_algorithm '$comp_clust.steps.clustering.S_algorithm'
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197 #if $comp_clust.steps.clustering.S_algorithm == 'fastANI'
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198 $comp_clust.steps.clustering.greedy_secondary_clustering
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199 #else if $comp_clust.steps.clustering.S_algorithm == 'ANImf'
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200 @NUCMER@
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201 @COVERAGE_METHOD@
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202 #else if $comp_clust.steps.clustering.S_algorithm == 'ANIn'
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203 @NUCMER@
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204 @COVERAGE_METHOD@
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205 #end if
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206 --S_ani $comp_clust.steps.S_ani
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207 --cov_thresh $comp_clust.steps.cov_thresh
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208 ]]></token>
0
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209
1
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210 <xml name="comparison_clustering_options">
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211 <section name="comp_clust" title="Genome comparison and clustering" expanded="false">
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212 <conditional name="steps">
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213 <param name="select" type="select" label="Steps in genome comparison">
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214 <option value="default" selected="true">Default: Run MASH clustering and a secondary clustering</option>
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215 <option value="SkipMash">Skip MASH clustering, just do secondary clustering on all genomes</option>
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216 <option value="SkipSecondary">Skip secondary clustering, just perform MASH clustering</option>
0
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217 </param>
1
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218 <when value="default">
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219 <expand macro="mash"/>
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220 <expand macro="secondary_clustering"/>
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221 </when>
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222 <when value="SkipMash">
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223 <expand macro="secondary_clustering"/>
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224 </when>
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225 <when value="SkipSecondary">
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226 <expand macro="mash"/>
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227 </when>
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228 </conditional>
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229 <param argument="--clusterAlg" type="select" label="Algorithm used to cluster genomes" help="Passed to scipy.cluster.hierarchy.linkage">
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230 <option value="average" selected="true">average</option>
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231 <option value="ward">ward</option>
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232 <option value="single">single</option>
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233 <option value="median">median</option>
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234 <option value="centroid">centroid</option>
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235 <option value="weighted">weighted</option>
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236 </param>
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237 <param argument="--run_tertiary_clustering" type='boolean' checked="false" truevalue='--run_tertiary_clustering' falsevalue='' label="Run an additional round of clustering on the final genome set?" help="This is especially useful when greedy clustering is performed and/or to handle cases where similar genomes end up in different primary clusters."/>
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238 </section>
0
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239 </xml>
1
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240 <xml name="test_default_comparison_clustering_options">
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241 <section name="comp_clust">
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242 <conditional name="steps">
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243 <param name="select" value="default" />
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244 <expand macro="test_default_mash"/>
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245 <expand macro="test_default_secondary_clustering"/>
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246 </conditional>
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247 <param name="clusterAlg" value="average"/>
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248 <param name="run_tertiary_clustering" value=''/>
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249 </section>
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250 </xml>
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251 <token name="@COMPARISON_CLUSTERING_OPTIONS@"><![CDATA[
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252 #if $comp_clust.steps.select == 'default'
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253 @MASH@
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254 @SECONDARY_CLUSTERING@
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255 #else if $comp_clust.steps.select == 'SkipMash'
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256 --SkipMash
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257 @SECONDARY_CLUSTERING@
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258 #else
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259 @MASH@
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260 --SkipSecondary
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261 #end if
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262 --clusterAlg '$comp_clust.clusterAlg'
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263 $comp_clust.run_tertiary_clustering
0
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264 ]]></token>
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265
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266 <xml name="scoring_options">
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267 <section name="scoring" title="Scoring criteria" expanded="false" help="Based off of the formula: A*Completeness - B*Contamination + C*(Contamination * (strain_heterogeneity/100)) + D*log(N50) + E*log(size) + F*(centrality - S_ani). With A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight; F = cent_weight">
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268 <param argument="--completeness_weight" type="float" value="1" label="Completeness weight"/>
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269 <param argument="--contamination_weight" type="float" value="5" label="Contamination weight"/>
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270 <param argument="--strain_heterogeneity_weight" type="float" value="1" min="0." max="1." label="Strain heterogeneity weight"/>
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271 <param argument="--N50_weight" type="float" value=".5" label="Weight of log(genome N50)"/>
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272 <param argument="--size_weight" type="float" value="0" label="Weight of log(genome size)"/>
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273 <param argument="--centrality_weight" type="float" value="1" label="Weight of (centrality - S_ani)"/>
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274 <param argument="--extra_weight_table" type="data" format="tabular" multiple="false" optional="true" label="Genome specific extra weight"/>
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275 </section>
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276 </xml>
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277 <xml name="test_default_scoring_options">
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278 <section name="scoring">
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279 <param name="completeness_weight" value="1"/>
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280 <param name="contamination_weight" value="5"/>
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281 <param name="strain_heterogeneity_weight" value="1"/>
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282 <param name="N50_weight" value=".5" />
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283 <param name="size_weight" value="0"/>
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284 <param name="centrality_weight" value="1"/>
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285 </section>
0
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286 </xml>
3
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287 <xml name="test_extra_weight_table_scoring_options">
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288 <section name="scoring">
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289 <param name="completeness_weight" value="1"/>
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290 <param name="contamination_weight" value="5"/>
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291 <param name="strain_heterogeneity_weight" value="1"/>
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292 <param name="N50_weight" value=".5" />
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293 <param name="size_weight" value="0"/>
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294 <param name="centrality_weight" value="1"/>
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295 <param name="extra_weight_table" ftype="tabular" value="extra_weight_table_test"/>
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296 </section>
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297 </xml>
0
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298 <token name="@SCORING_OPTIONS@"><![CDATA[
1
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299 --completeness_weight $scoring.completeness_weight
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300 --contamination_weight $scoring.contamination_weight
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301 --strain_heterogeneity_weight $scoring.strain_heterogeneity_weight
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302 --N50_weight $scoring.N50_weight
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303 --size_weight $scoring.size_weight
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304 --centrality_weight $scoring.centrality_weight
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305 #if str($extra_weight_table) != 'None'
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306 --extra_weight_table $extra_weight_table
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307 #end if
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308
0
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309 ]]></token>
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310
1
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311 <xml name="warning_options">
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312 <section name="warning" title="Warnings" expanded="false">
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313 <param argument="--warn_dist" type="float" value="0.25" min="0" max="1" label="How far from the threshold to throw cluster warnings"/>
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314 <param argument="--warn_sim" type="float" value="0.98" min="0" max="1" label="Similarity threshold for warnings between dereplicated genomes"/>
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315 <param argument="--warn_aln" type="float" value="0.25" min="0" max="1" label="Minimum aligned fraction for warnings between dereplicated genomes (ANIn)"/>
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316 </section>
0
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317 </xml>
1
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318 <xml name="test_default_warning_options">
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319 <section name="warning">
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320 <param name="warn_dist" value="0.25"/>
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321 <param name="warn_sim" value="0.98"/>
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322 <param name="warn_aln" value="0.25"/>
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323 </section>
0
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324 </xml>
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325 <token name="@WARNING_OPTIONS@"><![CDATA[
1
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326 --warn_dist $warning.warn_dist
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327 --warn_sim $warning.warn_sim
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328 --warn_aln $warning.warn_aln
0
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329 ]]></token>
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330
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331 <xml name="select_outputs">
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332 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
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333 <option value="log" selected="true">log</option>
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334 <option value="warnings" selected="true">Warnings</option>
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335 <option value="Primary_clustering_dendrogram" selected="true">Primary_clustering_dendrogram.pdf</option>
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336 <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option>
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337 <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option>
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338 <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option>
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339 <yield/>
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340 </param>
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341 </xml>
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342 <xml name="select_drep_outputs">
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343 <expand macro="select_outputs">
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344 <option value="Cluster_scoring">Cluster_scoring.pdf</option>
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345 <option value="Winning_genomes">Winning_genomes.pdf</option>
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346 <option value="Widb">Widb.csv</option>
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347 <option value="Chdb">Chdb.tsv</option>
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348 </expand>
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349 </xml>
1
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350 <xml name="test_default_select_drep_outputs">
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
351 <param name="select_outputs" value="log,warnings,Primary_clustering_dendrogram,Clustering_scatterplots,Cluster_scoring,Winning_genomes,Widb" />
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
352 </xml>
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
353 <xml name="test_default_select_outputs">
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
354 <param name="select_outputs" value="log,warnings,Primary_clustering_dendrogram,Clustering_scatterplots" />
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
355 </xml>
0
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
356
1
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
357 <xml name="common_outputs">
0
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
358 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
359 <filter>'log' in select_outputs or not select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
360 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
361 <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Warnings" from_work_dir="outdir/log/warnings.txt">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
362 <filter>'warnings' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
363 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
364 <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
365 <filter>'Primary_clustering_dendrogram' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
366 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
367 <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
368 <filter>'Secondary_clustering_dendrograms' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
369 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
370 <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
371 <filter>'Secondary_clustering_MDS' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
372 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
373 <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
374 <filter>'Clustering_scatterplots' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
375 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
376 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
377 <xml name="drep_outputs">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
378 <expand macro="common_outputs"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
379 <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
380 <filter>'Cluster_scoring' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
381 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
382 <data name="Winning_genomes" format="pdf" label="${tool.name} on ${on_string}: Winning_genomes.pdf" from_work_dir="outdir/figures/Winning_genomes.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
383 <filter>'Winning_genomes' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
384 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
385 <data name="Widb" format="csv" label="${tool.name} on ${on_string}: Widb.csv" from_work_dir="outdir/data_tables/Widb.csv">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
386 <filter>'Widb' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
387 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
388 <data name="Chdb" format="tabular" label="${tool.name} on ${on_string}: Chdb.tsv" from_work_dir="outdir/data/checkM/checkM_outdir/Chdb.tsv">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
389 <filter>'Chdb' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
390 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
391 </xml>
1
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
392 <xml name="test_string_inputs">
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
393 <param name="genomes" ftype="fasta" value="Enterococcus_casseliflavus_EC20.fasta,Enterococcus_faecalis_T2.fna,Enterococcus_faecalis_TX0104.fa"/>
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
394 </xml>
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
395 <xml name="test_integer_inputs">
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
396 <param name="genomes" ftype="fasta" value="001,002,003"/>
0
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
397 </xml>
1
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
398 <xml name="test_log_output">
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
399 <output name="log">
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
400 <assert_contents>
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
401 <yield/>
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
402 </assert_contents>
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
403 </output>
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
404 </xml>
0
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
405 <token name="@GENOMES_HELP@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
406 I/O PARAMETERS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
407 -g [GENOMES [GENOMES ...]], --genomes [GENOMES [GENOMES ...]]
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
408 genomes to cluster in .fasta format
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
409 (default: None)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
410
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
411
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
412 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
413 <token name="@FILTERING_HELP@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
414 FILTERING OPTIONS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
415 -l LENGTH, --length LENGTH
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
416 Minimum genome length
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
417 (default: 50000)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
418
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
419
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
420 -comp COMPLETENESS, --completeness COMPLETENESS
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
421 Minumum genome completeness
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
422 (default: 75)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
423
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
424
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
425 -con CONTAMINATION, --contamination CONTAMINATION
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
426 Maximum genome contamination
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
427 (default: 25)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
428
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
429
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
430 --ignoreGenomeQuality
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
431 Don't run checkM or do any quality filtering. NOT
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
432 RECOMMENDED! This is useful for use with
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
433 bacteriophages or eukaryotes or things where checkM
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
434 scoring does not work. Will only choose genomes based
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
435 on length and N50 (default: False)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
436
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
437
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
438 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
439 <token name="@GENOME_COMPARISON_HELP@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
440 GENOME COMPARISON PARAMETERS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
441 -ms MASH_SKETCH, --MASH_sketch MASH_SKETCH
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
442 MASH sketch size (default: 1000)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
443
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
444 --S_algorithm {goANI,ANIn,ANImf,gANI}
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
445 Algorithm for secondary clustering comaprisons:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
446 ANImf = (RECOMMENDED) Align whole genomes with nucmer; filter alignment; compare aligned regions
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
447 ANIn = Align whole genomes with nucmer; compare aligned regions
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
448 gANI = Identify and align ORFs; compare aligned ORFS
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
449 (default: ANImf)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
450
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
451 -n_PRESET {normal,tight}
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
452 Presets to pass to nucmer
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
453 tight = only align highly conserved regions
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
454 normal = default ANIn parameters (default: normal)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
455
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
456 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
457 <token name="@CLUSTERING_HELP@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
458 CLUSTERING PARAMETERS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
459 -pa P_ANI, --P_ani P_ANI
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
460 ANI threshold to form primary (MASH) clusters
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
461 (default: 0.9)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
462 -sa S_ANI, --S_ani S_ANI
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
463 ANI threshold to form secondary clusters
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
464 (default: 0.99)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
465
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
466 --SkipMash Skip MASH clustering, just do secondary clustering on
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
467 all genomes (default: False)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
468 --SkipSecondary Skip secondary clustering, just perform MASH clustering
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
469 (default: False)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
470
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
471 -nc COV_THRESH, --cov_thresh COV_THRESH
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
472 Minmum level of overlap between genomes when doing
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
473 secondary comparisons (default: 0.1)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
474 -cm {total,larger}, --coverage_method {total,larger}
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
475 Method to calculate coverage of an alignment
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
476 (for ANIn/ANImf only; gANI can only do larger method)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
477 total = 2*(aligned length) / (sum of total genome lengths)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
478 larger = max((aligned length / genome 1), (aligned_length / genome2))
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
479 (default: larger)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
480
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
481 --clusterAlg CLUSTERALG
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
482 Algorithm used to cluster genomes (passed to
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
483 scipy.cluster.hierarchy.linkage (default: average)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
484
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
485 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
486 <token name="@SCORING_HELP@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
487 SCORING CRITERIA
1
7157accd23d0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 5e6e589002d554be180e575080e9ad66cc78ed74"
iuc
parents: 0
diff changeset
488 Based off of the formula:
0
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
489 A*Completeness - B*Contamination + C*(Contamination * (strain_heterogeneity/100)) + D*log(N50) + E*log(size)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
490
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
491 A = completeness_weight; B = contamination_weight; C = strain_heterogeneity_weight; D = N50_weight; E = size_weight:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
492 -comW COMPLETENESS_WEIGHT, --completeness_weight COMPLETENESS_WEIGHT
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
493 completeness weight (default: 1)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
494 -conW CONTAMINATION_WEIGHT, --contamination_weight CONTAMINATION_WEIGHT
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
495 contamination weight (default: 5)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
496 -strW STRAIN_HETEROGENEITY_WEIGHT, --strain_heterogeneity_weight STRAIN_HETEROGENEITY_WEIGHT
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
497 strain heterogeneity weight (default: 1)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
498 -N50W N50_WEIGHT, --N50_weight N50_WEIGHT
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
499 weight of log(genome N50) (default: 0.5)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
500 -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
501 weight of log(genome size) (default: 0)
3
d99788b71ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 91d5bae878afa54d8264c1ca89c79b2d26ef35ad
iuc
parents: 2
diff changeset
502 -extraW EXTRA_WEIGHT_TABLE, --extra_weight_table EXTRA_WEIGHT_TABLE
d99788b71ce7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 91d5bae878afa54d8264c1ca89c79b2d26ef35ad
iuc
parents: 2
diff changeset
503 Path to a tab-separated file with two-columns, no headers, listing genome and extra score to apply to that genome (optional)
0
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
504
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
505
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
506 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
507 <token name="@TAXONOMY_HELP@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
508 TAXONOMY:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
509 --run_tax generate taxonomy information (Tdb)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
510 (default: False)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
511
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
512 --tax_method {percent,max}
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
513 Method of determining taxonomy
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
514 percent = The most descriptive taxonimic level with at least (per) hits
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
515 max = The centrifuge taxonomic level with the most overall hits
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
516 (default: percent)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
517
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
518
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
519 -per PERCENT, --percent PERCENT
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
520 minimum percent for percent method
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
521 (default: 50)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
522
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
523
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
524 --cent_index CENT_INDEX
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
525 path to centrifuge index (for example,
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
526 /home/mattolm/download/centrifuge/indices/b+h+v
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
527 (default: None)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
528
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
529 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
530 <token name="@WARNINGS_HELP@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
531 WARNINGS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
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532 --warn_dist WARN_DIST
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
533 How far from the threshold to throw cluster warnings
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
534 (default: 0.25)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
535 --warn_sim WARN_SIM Similarity threshold for warnings between dereplicated
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
536 genomes (default: 0.98)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
537 --warn_aln WARN_ALN Minimum aligned fraction for warnings between
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
538 dereplicated genomes (ANIn) (default: 0.25)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
539
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
540 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
541 </macros>