Mercurial > repos > iuc > dada2_assigntaxonomyaddspecies

annotate dada2_assignTaxonomyAddspecies.xml @ 0:18517edb4733 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
author iuc
date Fri, 08 Nov 2019 18:50:24 -0500
parents
children 1c9715cef808
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18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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1 <tool id="dada2_assignTaxonomyAddspecies" name="dada2: assignTaxonomy and addSpecies" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
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2 <description>Learn Error rates</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript '$dada2_script' \${GALAXY_SLOTS:-1}
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="dada2_script"><![CDATA[
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14 @READ_FOO@
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15
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16 library(dada2, quietly=T)
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17
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18 args <- commandArgs(trailingOnly = TRUE)
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19 nthreads <- as.integer(args[1])
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20
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21 seqs <- $read_data($seqs)
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22
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23 #if $reference_cond.reference_select == "history"
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24 ref <- '$reference_cond.refFasta'
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25 tl <- '$reference_cond.taxLevels'
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26 #else
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27 ref <- '$reference_cond.refFasta.fields.path'
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28 tl <- '$reference_cond.refFasta.fields.taxlevels'
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29 #end if
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30 tl <- strsplit(tl, ",")[[1]]
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31
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32 taxa <- assignTaxonomy(seqs, ref, minBoot = $minBoot, tryRC = $tryRC,
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33 outputBootstraps = $outputBootstraps,
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34 taxLevels = tl, multithread = nthreads, verbose=T)
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35
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36 #if $outputBootstraps
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37 boot <- taxa\$boot
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38 taxa <- taxa\$tax
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39 #end if
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40
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41 #if $addSpecies_cond.addSpecies_select == "TRUE"
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42 #if $addSpecies_cond.allowMultiple_cond.allowMultiple == "num"
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43 aM <- $addSpecies_cond.allowMultiple_cond.num
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44 #else
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45 aM <- $addSpecies_cond.allowMultiple_cond.allowMultiple
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46 #end if
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47 #if $addSpecies_cond.speciesreference_cond.speciesreference_select == "history"
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48 ref <- '$addSpecies_cond.speciesreference_cond.speciesrefFasta'
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49 #else
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50 ref <- '$addSpecies_cond.speciesreference_cond.speciesrefFasta.fields.path'
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51 #end if
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52 taxa <- addSpecies(taxa, ref, allowMultiple = aM, tryRC = $addSpecies_cond.tryRC)
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53 #end if
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54 write.table(taxa, file = '$output', quote = F, sep = "\t", row.names = T, col.names = NA)
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55
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56 #if $outputBootstraps
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57 write.table(boot, file = '$bootstraps', quote = F, sep = "\t", row.names = T, col.names = NA)
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58 #end if
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59 ]]></configfile>
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60 </configfiles>
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61 <inputs>
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62 <param name="seqs" type="data" format="@DADA_UNIQUES@,dada2_sequencetable,dada2_uniques" label="sequences to be assigned" help=""/>
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63 <conditional name="reference_cond">
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64 <param name="reference_select" type="select" label="Select a reference dataset your history or use a built-in?">
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65 <option value="builtin">Use a built-in reference</option>
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66 <option value="history">Use reference data from the history</option>
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67 </param>
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68 <when value="builtin">
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69 <param name="refFasta" type="select" label="Select reference data set" help="If a reference data set of interest is not listed, contact the Galaxy administrators">
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70 <options from_data_table="dada2_taxonomy">
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71 <filter type="sort_by" column="2"/>
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72 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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73 </options>
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74 </param>
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75 </when>
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76 <when value="history">
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77 <param name="refFasta" type="data" format="fasta,fasta.gz" label="Reference data set" />
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78 <param argument="taxLevels" type="text" label="Names of the taxonomic levels in the data set" help="comma separated list" />
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79 </when>
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80 </conditional>
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81 <param argument="minBoot" type="integer" value="50" min="0" label="Minimum bootstrap confidence" help="for assigning a
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82 taxonomic level"/>
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83 <param argument="tryRC" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Try reverse complement" help="the reverse-complement of each sequence will be used for classification if it is a better match to the reference sequences than the forward sequence"/>
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84 <param argument="outputBootstraps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Output bootstrap values"/>
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85
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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86 <conditional name="addSpecies_cond">
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
87 <param name="addSpecies_select" type="select" label="Add genus-species binomials to the taxonomic table">
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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88 <option value="FALSE">No</option>
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iuc
parents:
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89 <option value="TRUE">Yes</option>
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iuc
parents:
diff changeset
90 </param>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
91 <when value="FALSE"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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92 <when value="TRUE">
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
93 <conditional name="speciesreference_cond">
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
94 <param name="speciesreference_select" type="select" label="Select a reference dataset your history or use a built-in?">
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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95 <option value="builtin">Use a built-in reference</option>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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96 <option value="history">Use reference data from the history</option>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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97 </param>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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98 <when value="builtin">
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iuc
parents:
diff changeset
99 <param name="speciesrefFasta" argument="refFasta" type="select" label="Select reference data set" help="If a reference data set of interest is not listed, contact the Galaxy administrators">
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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100 <options from_data_table="dada2_species">
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iuc
parents:
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101 <filter type="sort_by" column="2"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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102 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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iuc
parents:
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103 </options>
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iuc
parents:
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104 </param>
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iuc
parents:
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105 </when>
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iuc
parents:
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106 <when value="history">
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iuc
parents:
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107 <param name="speciesrefFasta" argument="refFasta" type="data" format="fasta,fasta.gz" label="Reference data set" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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parents:
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108 </when>
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iuc
parents:
diff changeset
109 </conditional>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
110 <conditional name="allowMultiple_cond">
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iuc
parents:
diff changeset
111 <param argument="allowMultiple" type="select" label="reporting options">
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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112 <option value="FALSE">only unambiguous identifications</option>
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iuc
parents:
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113 <option value="TRUE">all exactly matched species</option>
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iuc
parents:
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114 <option value="num">specify the maximal number of reported exactly matched species</option>
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iuc
parents:
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115 </param>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
116 <when value="FALSE"/>
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iuc
parents:
diff changeset
117 <when value="TRUE"/>
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iuc
parents:
diff changeset
118 <when value="num">
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iuc
parents:
diff changeset
119 <param name="num" type="integer" value="" min="1" label="Number of matched species"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
120 </when>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
121 </conditional>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
122 <param argument="tryRC" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Try reverse complement" help="the reverse-complement of each sequence will be used for classification if it is a better match to the reference sequences than the forward sequence"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
123 </when>
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parents:
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124 </conditional>
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iuc
parents:
diff changeset
125 </inputs>
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iuc
parents:
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126 <outputs>
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iuc
parents:
diff changeset
127 <data name="output" format="tabular" label="${tool.name} on ${on_string}"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
128 <data name="bootstraps" format="tabular" label="${tool.name} on ${on_string}: bootstraps">
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iuc
parents:
diff changeset
129 <filter>outputBootstraps</filter>
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iuc
parents:
diff changeset
130 </data>
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iuc
parents:
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131 </outputs>
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iuc
parents:
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132 <tests>
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iuc
parents:
diff changeset
133 <!-- test w default params -->
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iuc
parents:
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134 <test expect_num_outputs="1">
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iuc
parents:
diff changeset
135 <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
136 <param name="reference_cond|reference_select" value="history"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
137 <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
138 <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
139 <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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140 <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
141 <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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142 <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" />
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iuc
parents:
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143 </test>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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144 <!-- test w default params, bulit in reference -->
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
145 <test expect_num_outputs="1">
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
146 <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
147 <param name="reference_cond|reference_select" value="builtin"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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148 <param name="reference_cond|refFasta" value="test_buildid"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
149 <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
150 <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="builtin"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
151 <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" value="test_buildid" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
152 <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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153 </test>
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iuc
parents:
diff changeset
154 <!-- test w output bootstraps, minRC, note: sim_size for bootstraps output due to the probabilistics -->
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
155 <test expect_num_outputs="2">
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
156 <param name="seqs" ftype="dada2_sequencetable" value="removeBimeraDenovo_F3D0.tab"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
157 <param name="reference_cond|reference_select" value="history"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
158 <param name="reference_cond|refFasta" ftype="fasta" value="reference.fa"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
159 <param name="reference_cond|taxLevels" value="Level1,Level2,Level3,Level4,Level5" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
160 <param name="minBoot" value="42" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
161 <param name="tryRC" value="TRUE" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
162 <param name="outputBootstraps" value="TRUE" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
163 <param name="addSpecies_cond|addSpecies_select" value="TRUE"/>
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iuc
parents:
diff changeset
164 <param name="addSpecies_cond|speciesreference_cond|speciesreference_select" value="history"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
165 <param name="addSpecies_cond|speciesreference_cond|speciesrefFasta" ftype="fasta" value="reference_species.fa" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
166 <param name="addSpecies_cond|allowMultiple" value="TRUE"/>
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
167 <param name="addSpecies_cond|tryRC" value="TRUE" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
168 <output name="output" value="assignTaxonomyAddspecies_F3D0.tab" ftype="tabular" compare="sim_size" />
18517edb4733 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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169 <output name="bootstraps" value="assignTaxonomyAddspecies_F3D0_boot.tab" ftype="tabular" compare="sim_size" />
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170 </test>
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171 </tests>
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172 <help><![CDATA[
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173 Description
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174 ...........
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175
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176 This tool implements dada2's assignTaxonomy and assignSpecies functions.
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177
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178 - assignTaxonomy assigns taxonomy to the sequence variants. The DADA2 package provides a native implementation of the naive Bayesian classifier method for this purpose (see Wang et al. 2007, kmer size 8 and 100 bootstrap replicates). The assignTaxonomy function takes as input a set of sequences to be classified and a training set of reference sequences with known taxonomy, and outputs taxonomic assignments with at least minBoot bootstrap confidence. Properly formatted reference files for several popular taxonomic databases are available http://benjjneb.github.io/dada2/training.html
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179 - assignSpecies makes species level assignments based on exact matching between ASVs and sequenced reference strains. Recent analysis suggests that exact matching (or 100% identity) is the only appropriate way to assign species to 16S gene fragments. Currently, species-assignment training fastas are available for the Silva and RDP 16S databases.
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180
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181 Usage
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182 .....
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183
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184 **Input**
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185
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186 - A list of sequences contained in the results of removeBimeraDenovo or sequenceTable (note that also the results of dada, and mergePairs are accepted).
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187 - Reference data bases for taxonomic and species/genus level assignment. Several cached data bases can be chosen (ask your Galaxy admin if they are missing). For using custom data bases see below.
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188
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189 **Output**
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190
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191 - A table containing the assigned taxonomies exceeding the minBoot level of bootstrapping confidence. Rows correspond to the provided sequences, columns to the taxonomic levels. NA indicates that the sequence was not consistently classified at that level at the minBoot threshold.
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192 - Optionally two columns for the genus and species taxonomic levels can be added. NA indicates that the sequence was not classified at that level.
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193 - If outputBootstraps checked, a table containing the assigned taxonomies (named "taxa") and the bootstrap values (named "boot") will be returned.
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194
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195 @HELP_OVERVIEW@
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196
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197 Custom Reference data sets
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198 ..........................
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199
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200 For ** taxonomy assignment ** the following is needed:
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201
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202 - a reference fasta data base
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203 - a comma separated list of taxonomic ranks present in the reference data base
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204
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205 The reference fasta data base for taxonomic assignment (fasta or compressed fasta) needs to encode the taxonomy corresponding to each sequence in the fasta header lines in the following fashion (note, the second sequence is not assigned down to level 6):
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206
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207 ::
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208
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209 >Level1;Level2;Level3;Level4;Level5;Level6;
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210 ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC
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211 >Level1;Level2;Level3;Level4;Level5;
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212 CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC
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213
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214 The list of required taxonomic ranks could be for instance: "Kingdom,Phylum,Class,Order,Family,Genus"
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215
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216 The reference data base for ** species assignment ** is a fasta file (or compressed fasta file), with the id line formatted as follows:
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217
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218 ::
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219
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220 >ID Genus species
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221 ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC
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222 >ID Genus species
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223 CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC
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224
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225
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226 ]]></help>
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227 <expand macro="citations">
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228 <citation type="doi">10.1128/AEM.00062-07</citation>
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229 </expand>
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230 </tool>
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231
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232