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annotate metaphlan2.xml @ 0:d2448d2bf1f8 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
author bebatut
date Wed, 01 Jun 2016 10:45:26 -0400
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children 8991e05c44e4
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1 <tool id="metaphlan2" name="MetaPhlAn2" version="2.5.0">
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3 <description>to profile the composition of microbial communities</description>
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5 <macros>
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6 <import>metaphlan2_macros.xml</import>
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7 </macros>
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8
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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12 <version_command>
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13 <![CDATA[
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14 metaphlan2.py -v
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15 ]]>
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16 </version_command>
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18 <command>
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19 <![CDATA[
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20 (which bowtie2 || exit 200)
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22 &&
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24 #if $db.db_selector == "history"
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25 mkdir ref_db
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26 &&
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27 bowtie2-build $db.db_sequences ref_db/ref_db
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28 &&
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29 python $__tool_directory__/transform_json_to_pkl.py
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30 --json_input $db_metadata
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31 --pkl_output ref_db/metadata.pkl
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32 &&
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33 #end if
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34
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35 metaphlan2.py
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36 $input_file
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37 -o $output_file
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38 --input_type ${input_file.datatype.file_ext}
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39
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40 --bowtie2_exe `which bowtie2`
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41
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42 #if $db.db_selector == "cached"
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43 #set $table = dict([(_[0], _[2]) for _ in $db.cached_db.input.options.tool_data_table.data])
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44 #set $db_choice = $db.cached_db.value
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45 --bowtie2db $table[$db_choice]
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46 --mpa_pkl $table[$db_choice]".pkl"
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47 #else
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48 --bowtie2db ref_db/ref_db
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49 --mpa_pkl ref_db/metadata.pkl
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50 #end if
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51
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52 --no_map
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53
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54 -t $analysis_type.analysis_type_select
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55 #if $analysis_type.analysis_type_select == "rel_ab"
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56 --tax_lev $analysis_type.taxonomic_level
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57 #else if $analysis_type.analysis_type_select == "marker_ab_table"
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58 --nreads $analysis_type.nreads
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59 #else if $analysis_type.analysis_type_select == "marker_pres_table"
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60 --pres_th $analysis_type.pres_th
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61 #end if
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62
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63 --min_cu_len $min_cu_len
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64 --min_alignment_len $min_alignment_len
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65
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66 $ignore_viruses
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67 $ignore_eukaryotes
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68 $ignore_bacteria
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69 $ignore_archaea
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70
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71 --stat_q $stat_q
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72 -s $sam_output_file
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73 ]]>
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74 </command>
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75
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76 <inputs>
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77 <param name="input_file" type="data" format="fastq,fasta,sam" label="Input file" help=""/>
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78
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79 <conditional name="db">
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80 <param name="db_selector" type="select" label="Database with clade-specific marker genes" help="">
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81 <option value="cached" selected="true">Locally cached</option>
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82 <option value="history">From history</option>
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83 </param>
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84
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85 <when value="cached">
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86 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select" >
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87 <options from_data_table="metaphlan2_db" />
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88 </param>
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89 </when>
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90 <when value="history">
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91 <param name="db_sequences" type="data" format="fasta" label="Database with clade-specific marker genes from history" help="(--bowtie2db)"/>
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92 <param name="db_metadata" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history" help="(--mpa_pkl)"/>
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93 </when>
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94 </conditional>
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95
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96 <conditional name="analysis_type">
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97 <param name="analysis_type_select" type="select" label="Type of analysis to perform" help="(-t)">
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98 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
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99 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
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100 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
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101 <option value="marker_ab_table">Normalized marker counts (only when > 0.0 and normalized by metagenome size if --nreads is specified)</option>
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102 <option value="marker_counts">Non-normalized marker counts (use with extreme caution)</option>
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103 <option value="marker_pres_table">List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
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104 </param>
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105
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106 <when value="rel_ab">
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107 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output" help="(--tax_lev)">
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108 <option value="a" selected="true">All taxonomic levels</option>
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109 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
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110 <option value="p">Phyla only</option>
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111 <option value="c">Classes only</option>
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112 <option value="o">Orders only</option>
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113 <option value="f">Families only</option>
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114 <option value="g">Genera only</option>
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115 <option value="s">Species only</option>
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116 </param>
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117 </when>
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118
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119 <when value="reads_map"/>
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120 <when value="clade_profiles"/>
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121
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122 <when value="marker_ab_table">
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123 <param name="nreads" type="integer" value="0" label="Total number of reads in the original metagenome" help="It is used for normalizing the length-normalized counts with the metagenome size as well. No normalization applied if the value is not specified"/>
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124 </when>
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125
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126 <when value="marker_counts"/>
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127
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128 <when value="marker_pres_table">
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129 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
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130 </when>
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131 </conditional>
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132
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133 <param name="min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances" help=""/>
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134
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135 <param name="min_alignment_len" type="integer" value="0" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded." help=""/>
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136
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137 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
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138 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
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139
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140 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
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141
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142 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
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143
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144 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
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145 </inputs>
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146
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147 <outputs>
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148 <data format="tabular" name="output_file" label="${tool.name} on ${on_string}: Community profile" />
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149 <data format="sam" name="sam_output_file" label="${tool.name} on ${on_string}: Sam file" />
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150 </outputs>
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151
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152 <tests>
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153 <test>
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154 <param name="input_file" value="input_sequences.fasta"/>
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155 <param name="db_selector" value="history" />
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156 <param name="db_metadata" value="marker_metadata.json" />
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157 <param name="db_sequences" value="marker_sequences.fasta" />
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158 <param name="analysis_type_select" value="rel_ab" />
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159 <param name="taxonomic_level" value="a" />
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160 <param name="min_cu_len" value="2000" />
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161 <param name="min_alignment_len" value="0" />
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162 <param name="ignore_viruses" value="" />
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163 <param name="ignore_eukaryotes" value="" />
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164 <param name="ignore_bacteria" value="" />
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165 <param name="ignore_archaea" value="" />
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166 <param name="stat_q" value="0.1" />
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167 <output name="output_file" file="community_profile.tabular"/>
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168 </test>
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169 </tests>
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170
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171 <help><![CDATA[
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172 **What it does**
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173
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174 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
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175
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176 **Inputs**
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177
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178 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced SAM file.
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179
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180 It is also possible to use a custom database with clade-specific marker genes. In this case, a fasta file with marker gene sequences is required and also a file containing metadata. This file is a json file with:
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181
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182 ::
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183
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184 {
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185 "taxonomy": {
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186 "taxonomy of genome1": genome1_length,
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187 "taxonomy of genome2": genome2_length,
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188 ...
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189 }
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190 "markers": {
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191 "marker1_name": {
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192 "clade": the clade that the marker belongs to,
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193 "ext": [list of external genomes where the marker appears],
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194 "len": length of the marker,
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195 "score": score of the marker,
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196 "taxon": the taxon of the marker
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197 }
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198 ...
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199 }
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200 }
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201
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202 The marker names correspond to sequence name in corresponding fasta file with marker gene sequences.
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203
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204 **Outputs**
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205
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206 The main output file is a tab-separated output file of the predicted taxon relative abundances.
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207
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208 ]]></help>
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209
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210 <citations>
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211 <citation type="doi">10.1038/nmeth.3589</citation>
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212 </citations>
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213 </tool>