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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
author iuc
date Tue, 05 May 2020 06:20:45 -0400
parents
children 7157accd23d0
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ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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1 <macros>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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2 <token name="@VERSION@">2.5.4</token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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3 <xml name="requirements">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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4 <requirements>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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5 <requirement type="package" version="@VERSION@">drep</requirement>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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6 <yield/>
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7 </requirements>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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8 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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9 <xml name="citations">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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10 <citations>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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11 <citation type="doi">10.1038/ismej.2017.126</citation>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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12 <yield />
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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13 </citations>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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14 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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15
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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16
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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17 <xml name="genomes">
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18 <param argument="--genomes" type="data" format="fasta" label="genomes fasta files" multiple="true"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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19 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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20 <token name="@PREPARE_GENOMES@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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21 #import re
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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22 #set $genomefiles = []
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23 #for $genome in $genomes
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24 #set $input_name = $re.sub('[^\w\-_.]', '_',str($genome.element_identifier.split('/')[-1]))
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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25 ln -s '${genome}' '${input_name}' &&
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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26 $genomefiles.append($input_name)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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27 #end for
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28 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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29 <token name="@GENOMES@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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30 -g
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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31 #for $genomefile in $genomefiles
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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32 '${genomefile}'
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33 #end for
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34 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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35
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36
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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37 <xml name="checkm_method">
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38 <param argument="--checkM_method" type="select" label="checkm method" optional="true">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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39 <option value="taxonomy_wf">taxonomy_wf (faster)</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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40 <option value="lineage_wf">lineage_wf (more accurate)</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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41 </param>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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42 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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43 <token name="@CHECKM_METHOD@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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44 #if $checkM_method:
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45 --checkM_method $checkM_method
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46 #end if
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47 ]]></token>
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48
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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49 <xml name="filtering_options">
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50 <conditional name="filter">
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51 <param name="set_options" type="select" label="set filtering options">
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52 <option value="yes">Yes</option>
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53 <option value="no" selected="true">No (use --checkM_method taxonomy_wf)</option>
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54 </param>
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55 <when value="yes">
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56 <param argument="--length" type="integer" value="50000" label="Minimum genome length"/>
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57 <param argument="--completeness" type="integer" value="75" min="0" max="100" label="Minimum genome completeness percent"/>
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58 <param argument="--contamination" type="integer" value="25" min="0" max="100" label="Maximum genome contamination percent"/>
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59
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60 <conditional name="quality">
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61 <param argument="source" type="select" label="genome quality">
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62 <help>
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63 --ignoreGenomeQuality is useful with
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64 bacteriophages or eukaryotes or things where checkM
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65 scoring does not work. Will only choose genomes based
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66 on length and N50.
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67 </help>
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68 <option value="checkm" selected="true">Run checkM</option>
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69 <option value="genomeInfo">User supplied genomeInfo csv file</option>
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70 <option value="ignoreGenomeQuality">--ignoreGenomeQuality (NOT RECOMMENDED!)</option>
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71 </param>
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72 <when value="checkm">
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73 <param argument="--checkM_method" type="select" label="checkm method" optional="true">
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74 <help>
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75 Using the checkm method of lineage_wf can require more than 40Gb of RAM.
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76 </help>
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77 <option value="taxonomy_wf">taxonomy_wf (faster)</option>
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78 <option value="lineage_wf">lineage_wf (more accurate)</option>
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79 </param>
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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="genomes fasta files">
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83 <help><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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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>
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89 </param>
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90 </when>
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91 <when value="ignoreGenomeQuality"/>
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92 </conditional>
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93 </when>
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94 <when value="no"/>
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95 </conditional>
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96 </xml>
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97 <token name="@FILTER_OPTIONS@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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98 #if $filter.set_options == 'yes':
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99 --length $filter.length
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100 --completeness $filter.completeness
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101 --contamination $filter.contamination
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102 #if $filter.quality.source == 'checkm'
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103 --checkM_method $filter.quality.checkM_method
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104 #elif $filter.quality.source == 'genomeInfo'
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105 --genomeInfo $filter.quality.genomeInfo
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106 #elif $filter.quality.source == 'ignoreGenomeQuality'
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107 --ignoreGenomeQuality
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108 #end if
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109 #else
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110 --checkM_method taxonomy_wf
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111 #end if
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112 ]]></token>
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113
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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114 <xml name="genome_comparison_options">
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115 <conditional name="genome_comparison">
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116 <param name="set_options" type="select" label="set genome comparison options">
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117 <option value="yes">Yes</option>
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118 <option value="no" selected="true">No</option>
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119 </param>
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120 <when value="yes">
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121 <param argument="--MASH_sketch" type="integer" value="1000" label="MASH sketch size"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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122 <param argument="--S_algorithm" type="select" label="Algorithm for secondary clustering comaprisons">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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123 <option value="ANImf" selected="true">ANImf = (RECOMMENDED) Align whole genomes with nucmer; filter alignment; compare aligned regions</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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124 <option value="ANIn">ANIn = Align whole genomes with nucmer; compare aligned regions</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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125 <option value="gANI">gANI = Identify and align ORFs; compare aligned ORFS</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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126 </param>
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127 <param argument="-n_PRESET" type="select" label="Presets to pass to nucmer">
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128 <option value="normal" selected="true">normal = default ANIn parameters (default: normal)</option>
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129 <option value="tight">tight = only align highly conserved regions</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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130 </param>
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131 </when>
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132 <when value="no"/>
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133 </conditional>
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134 </xml>
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135 <token name="@GENOME_COMPARISON_OPTIONS@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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136 #if $genome_comparison.set_options == 'yes':
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iuc
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137 --MASH_sketch $genome_comparison.MASH_sketch
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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138 --S_algorithm $genome_comparison.S_algorithm
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139 -n_PRESET $genome_comparison.n_PRESET
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140 #end if
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141 ]]></token>
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142
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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143 <xml name="clustering_options">
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144 <conditional name="clustering">
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145 <param name="set_options" type="select" label="set clustering options">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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146 <option value="yes">Yes</option>
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147 <option value="no" selected="true">No</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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148 </param>
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149 <when value="yes">
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150 <param argument="--P_ani" type="float" value="0.9" min="0." max="1." label="ANI threshold to form primary (MASH) clusters"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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151 <param argument="--S_ani" type="float" value="0.99" min="0." max="1." label="ANI threshold to form secondary clusters"/>
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152
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153 <param argument="--SkipMash" type="boolean" truevalue="--SkipMash" falsevalue="" checked="false" label="Skip MASH clustering, just do secondary clustering on all genomes"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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154 <param argument="--SkipSecondary" type="boolean" truevalue="--SkipSecondary" falsevalue="" checked="false" label="Skip secondary clustering, just perform MASH clustering"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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155 <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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156 <param argument="--coverage_method" type="select" label="Method to calculate coverage of an alignment">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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157 <help>(for ANIn/ANImf only; gANI can only do larger method)</help>
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158 <option value="larger" selected="true">arger = max((aligned length / genome 1), (aligned_length / genome2))</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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159 <option value="total">total = 2*(aligned length) / (sum of total genome lengths)</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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160 </param>
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parents:
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161 <param argument="--clusterAlg" type="select" label="Algorithm used to cluster genomes">
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162 <help>(passed to scipy.cluster.hierarchy.linkage)</help>
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163 <option value="average" selected="true">average</option>
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164 </param>
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165 </when>
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166 <when value="no"/>
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167 </conditional>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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168 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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169 <token name="@CLUSTERING_OPTIONS@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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170 #if $clustering.set_options == 'yes':
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171 --P_ani $clustering.P_ani
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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172 --S_ani $clustering.S_ani
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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173 $clustering.SkipMash
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174 $clustering.SkipSecondary
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175 --cov_thresh $clustering.cov_thresh
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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176 --coverage_method $clustering.coverage_method
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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177 --clusterAlg $clustering.clusterAlg
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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178 #end if
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
179 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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180
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
181 <xml name="scoring_options">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
182 <conditional name="scoring">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
183 <param name="set_options" type="select" label="set scoring options">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
184 <option value="yes">Yes</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
185 <option value="no" selected="true">No</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
186 </param>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
187 <when value="yes">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
188 <param argument="--completeness_weight" type="float" value="1" label="completeness weight">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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189 <help>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
190 Based off of the formula:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
191 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
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diff changeset
192 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"
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193 </help>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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194 </param>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
195 <param argument="--contamination_weight" type="float" value="5" label="contamination weight"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
196 <param argument="--strain_heterogeneity_weight" type="float" value="1" min="0." max="1." label="strain heterogeneity weight"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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197 <param argument="--N50_weight" type="float" value=".5" label="weight of log(genome N50)"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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198 <param argument="--size_weight" type="float" value="0" label="weight of log(genome size)"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
199 </when>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
200 <when value="no"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
201 </conditional>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
202 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
203 <token name="@SCORING_OPTIONS@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
204 #if $scoring.set_options == 'yes':
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
205 --completeness_weight $scoring.completeness_weight
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
206 --contamination_weight $scoring.contamination_weight
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
207 --strain_heterogeneity_weight $scoring.strain_heterogeneity_weight
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
208 --N50_weight $scoring.N50_weight
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
209 --size_weight $scoring.size_weight
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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210 #end if
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
211 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
212
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
213 <xml name="taxonomy_options">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
214 <conditional name="taxonomy">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
215 <param name="set_options" type="select" label="generate taxonomy information">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
216 <option value="yes">Yes</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
217 <option value="no" selected="true">No</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
218 </param>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
219 <when value="yes">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
220 <param argument="--tax_method" type="select" label="Method of determining taxonomy">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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221 <help>(for ANIn/ANImf only; gANI can only do larger method)</help>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
222 <option value="percent" selected="true">percent = The most descriptive taxonimic level with at least (per) hits</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
223 <option value="max">max = The centrifuge taxonomic level with the most overall hits</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
224 </param>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
225 <param argument="--percent" type="float" value="50" min="0" max="100" label="minimum percent for percent method"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
226 <param argument="--cent_index" type="data" format="" label="centrifuge index"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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227 </when>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
228 <when value="no"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
229 </conditional>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
230 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
231 <token name="@TAXONOMY_OPTIONS@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
232 #if $taxonomy.set_options == 'yes':
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
233 --run_tax
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
234 --tax_method $taxonomy.tax_method
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
235 --percent $taxonomy.percent
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
236 --cent_index $taxonomy.cent_index
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
237 #end if
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
238 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
239
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
240 <xml name="warning_options">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
241 <conditional name="warning">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
242 <param name="set_options" type="select" label="set warning options">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
243 <option value="yes">Yes</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
244 <option value="no" selected="true">No</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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diff changeset
245 </param>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
246 <when value="yes">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
247 <param argument="--warn_dist" type="float" value="0.25" min="0" max="1" label="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
248 <param argument="--warn_sim" type="float" value="0.98" min="0" max="1" label="Similarity threshold for warnings between dereplicated genomes"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
249 <param argument="--warn_aln" type="float" value="0.25" min="0" max="1" label="Minimum aligned fraction for warnings between dereplicated genomes (ANIn)"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
250 </when>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
251 <when value="no"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
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diff changeset
252 </conditional>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
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parents:
diff changeset
253 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
254 <token name="@WARNING_OPTIONS@"><![CDATA[
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
255 #if $warning.set_options == 'yes':
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
256 --warn_dist $warning.warn_dist
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
257 --warn_sim $warning.warn_sim
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
258 --warn_aln $warning.warn_aln
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
259 #end if
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
260 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
261
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
262 <xml name="select_outputs">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
263 <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
264 <option value="log" selected="true">log</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
265 <option value="warnings" selected="true">Warnings</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
266 <option value="Primary_clustering_dendrogram" selected="true">Primary_clustering_dendrogram.pdf</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
267 <option value="Secondary_clustering_dendrograms">Secondary_clustering_dendrograms.pdf</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
268 <option value="Secondary_clustering_MDS">Secondary_clustering_MDS.pdf</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
269 <option value="Clustering_scatterplots" selected="true">Clustering_scatterplots.pdf</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
270 <yield/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
271 </param>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
272 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
273 <xml name="select_drep_outputs">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
274 <expand macro="select_outputs">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
275 <option value="Cluster_scoring">Cluster_scoring.pdf</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
276 <option value="Winning_genomes">Winning_genomes.pdf</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
277 <option value="Widb">Widb.csv</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
278 <option value="Chdb">Chdb.tsv</option>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
279 </expand>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
280 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
281
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
282 <xml name="common_outputs">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
283 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="outdir/log/logger.log">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
284 <filter>'log' in select_outputs or not select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
285 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
286 <data name="warnings" format="txt" label="${tool.name} on ${on_string}: Warnings" from_work_dir="outdir/log/warnings.txt">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
287 <filter>'warnings' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
288 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
289 <data name="Primary_clustering_dendrogram" format="pdf" label="${tool.name} on ${on_string}: Primary_clustering_dendrogram.pdf" from_work_dir="outdir/figures/Primary_clustering_dendrogram.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
290 <filter>'Primary_clustering_dendrogram' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
291 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
292 <data name="Secondary_clustering_dendrograms" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_dendrograms.pdf" from_work_dir="outdir/figures/Secondary_clustering_dendrograms.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
293 <filter>'Secondary_clustering_dendrograms' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
294 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
295 <data name="Secondary_clustering_MDS" format="pdf" label="${tool.name} on ${on_string}: Secondary_clustering_MDS.pdf" from_work_dir="outdir/figures/Secondary_clustering_MDS.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
296 <filter>'Secondary_clustering_MDS' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
297 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
298 <data name="Clustering_scatterplots" format="pdf" label="${tool.name} on ${on_string}: Clustering_scatterplots.pdf" from_work_dir="outdir/figures/Clustering_scatterplots.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
299 <filter>'Clustering_scatterplots' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
300 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
301 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
302
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
303
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
304 <xml name="drep_outputs">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
305 <expand macro="common_outputs"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
306 <data name="Cluster_scoring" format="pdf" label="${tool.name} on ${on_string}: Cluster_scoring.pdf" from_work_dir="outdir/figures/Cluster_scoring.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
307 <filter>'Cluster_scoring' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
308 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
309 <data name="Winning_genomes" format="pdf" label="${tool.name} on ${on_string}: Winning_genomes.pdf" from_work_dir="outdir/figures/Winning_genomes.pdf">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
310 <filter>'Winning_genomes' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
311 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
312 <data name="Widb" format="csv" label="${tool.name} on ${on_string}: Widb.csv" from_work_dir="outdir/data_tables/Widb.csv">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
313 <filter>'Widb' in select_outputs</filter>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
314 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
315 <data name="Chdb" format="tabular" label="${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
316 <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
317 </data>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
318 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
319
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
320
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
321 <xml name="test_defaults_log">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
322 <test>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
323 <param name="genomes" ftype="fasta" value="Enterococcus_casseliflavus_EC20.fasta,Enterococcus_faecalis_T2.fna,Enterococcus_faecalis_TX0104.fa"/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
324 <output name="log">
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
325 <assert_contents>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
326 <yield/>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
327 </assert_contents>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
328 </output>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
329 </test>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
330 </xml>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
331
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
332 <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
333 I/O PARAMETERS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
334 -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
335 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
336 (default: None)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
337
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
338
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
339 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
340
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
341 <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
342 FILTERING OPTIONS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
343 -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
344 Minimum genome length
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
345 (default: 50000)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
346
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
347
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
348 -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
349 Minumum genome completeness
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
350 (default: 75)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
351
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
352
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
353 -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
354 Maximum genome contamination
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
355 (default: 25)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
356
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
357
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
358 --ignoreGenomeQuality
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
359 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
360 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
361 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
362 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
363 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
364
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
365
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
366 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
367
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
368 <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
369 GENOME COMPARISON PARAMETERS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
370 -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
371 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
372
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
373 --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
374 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
375 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
376 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
377 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
378 (default: ANImf)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
379
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
380 -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
381 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
382 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
383 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
384
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
385 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
386
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
387 <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
388 CLUSTERING PARAMETERS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
389 -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
390 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
391 (default: 0.9)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
392 -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
393 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
394 (default: 0.99)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
395
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
396 --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
397 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
398 --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
399 (default: False)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
400
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
401 -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
402 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
403 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
404 -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
405 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
406 (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
407 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
408 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
409 (default: larger)
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 --clusterAlg CLUSTERALG
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
412 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
413 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
414
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
415 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
416
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
417 <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
418 SCORING CRITERIA
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
419 Based off of the formula:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
420 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
421
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
422 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
423 -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
424 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
425 -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
426 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
427 -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
428 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
429 -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
430 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
431 -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
432 weight of log(genome size) (default: 0)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
433
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
434
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
435 ]]></token>
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 <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
438 TAXONOMY:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
439 --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
440 (default: False)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
441
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
442 --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
443 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
444 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
445 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
446 (default: percent)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
447
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
448
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
449 -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
450 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
451 (default: 50)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
452
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
453
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
454 --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
455 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
456 /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
457 (default: None)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
458
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
459 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
460
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
461 <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
462 WARNINGS:
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
463 --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
464 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
465 (default: 0.25)
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
466 --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
467 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
468 --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
469 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
470
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
471 ]]></token>
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
472
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
473
ef1c257adcbd "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 8fa5ff35b45c2b046c7f4800410cf39cb89a299a"
iuc
parents:
diff changeset
474 </macros>