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annotate metaphlan2.xml @ 9:31dd7ace2be4 draft

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author bebatut
date Thu, 05 Nov 2015 08:44:11 -0500
parents 2d1a20517280
children ebe6b7fab320
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1 <tool id="metaphlan2" name="MetaPhlAn2" version="0.1.0">
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3 <description>to profile the composition of microbial communities</description>
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5 <requirements>
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6 <requirement type="package" version="2.2.5">bowtie2</requirement>
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7 <requirement type="package" version="2.0">metaphlan2</requirement>
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8 </requirements>
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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14 <version_command>
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15 <![CDATA[
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16 python \${METAPHLAN2_DIR}/metaphlan.py -v
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17 ]]>
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18 </version_command>
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20 <command>
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21 <![CDATA[
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22 python \${METAPHLAN2_DIR}/metaphlan.py
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23 $input_file
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24 -o $output_file
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26 --input_type ${input_file.datatype.file_ext}
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27 --mpa_pkl \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200.pkl
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28 --bowtie2db \${METAPHLAN2_DIR}/db_v20/mpa_v20_m200
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30 $bowtie2_output
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31 #if $bowtie2_output == ''
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32 --bowtie2out $bowtie2_output
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33 #end if
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35 -t $analysis_type
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37 #if $analysis_type.analysis_type_select == "rel_ab"
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38 --tax_lev $analysis_type.taxonomic_level
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39 #else if $analysis_type.analysis_type_select == "marker_ab_table"
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40 --nreads $analysis_type.nreads
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41 #else if $analysis_type.analysis_type_select == "marker_pres_table"
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42 --pres_th $analysis_type.pres_th
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43 #end if
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45 --min_cu_len $min_cu_len
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46 --min_alignment_len $min_alignment_len
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48 $ignore_viruses
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49 $ignore_eukaryotes
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50 $ignore_bacteria
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51 $ignore_archaea
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53 --stat_q $stat_q
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54
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55 #if $sam_output
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56 -s $sam_output_file
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57 #end if
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59 #if $biom_output
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60 -biom $biom_output_file
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61 #end if
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62 ]]>
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63 </command>
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64
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65 <inputs>
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66 <param name="input_file" type="data" format="fastq,fasta,sam,bowtie2out" label="Input file" help=""/>
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67
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68 <conditional name="analysis_type">
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69 <param name="analysis_type_select" type="select" label="Type of analysis to perform">
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70 <option value="rel_ab" selected="true">Profiling a metagenomes in terms of relative abundances</option>
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71 <option value="rel_ab_w_read_stats">Profiling a metagenomes in terms of relative abundances and estimate the number of reads comming from each clade</option>
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72 <option value="reads_map">Mapping from reads to clades (only reads hitting a marker)</option>
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73 <option value="clade_profiles">Normalized marker counts for clades with at least a non-null marker</option>
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74 <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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75 <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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76 </param>
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77 <when value="rel_ab">
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78 <param name="taxonomic_level" type="select" label="Taxonomic level for the relative abundance output">
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79 <option value="a" selected="true">All taxonomic levels</option>
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80 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
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81 <option value="p">Phyla only</option>
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82 <option value="c">Classes only</option>
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83 <option value="o">Orders only</option>
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84 <option value="f">Families only</option>
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85 <option value="g">Genera only</option>
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86 <option value="s">Species only</option>
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87 </param>
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88 </when>
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89 <when value="marker_ab_table">
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90 <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"/>
0
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91 </when>
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92 <when value="marker_pres_table">
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93 <param name="pres_th" type="integer" value="0" label=" Threshold for calling a marker present" help=""/>
0
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94 </when>
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95 </conditional>
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96
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97 <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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98
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99 <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=""/>
0
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100
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101 <param name="ignore_viruses" type='boolean' checked="true" truevalue='' falsevalue='--ignore_viruses' label="Profile viral organisms?" help="" />
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102 <param name="ignore_eukaryotes" type='boolean' checked="true" truevalue='' falsevalue='--ignore_eukaryotes' label="Profile eukaryotic organisms?" help="" />
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103 <param name="ignore_bacteria" type='boolean' checked="true" truevalue='' falsevalue='--ignore_bacteria' label="Profile bacteria organisms?" help="" />
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104 <param name="ignore_archaea" type='boolean' checked="true" truevalue='' falsevalue='--ignore_archaea' label="Profile archea organisms?" help="" />
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105
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106 <param name="stat_q" type="float" value="0.1" label="Quantile value for the robust average" help=""/>
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107
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108 <param name="bowtie2_output" type='boolean' checked="true" truevalue="" falsevalue='--no_map' label="Store the output of BowTie2?" help="" />
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109 <param name="sam_output" type='boolean' label="Output a sam file?" help="" />
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110 <param name="biom_output" type='boolean' label="Output a biom file?" help="" />
0
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111 </inputs>
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112
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113 <outputs>
9
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114 <data format="txt" name="output_file"
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115 metadata="input_sequence_file"
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116 label="Profile of communities on ${on_string} (MetaPhlAn)" />
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117
9
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118 <data format="bowtie2" name="bowtie2_output_file"
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119 metadata="input_sequence_file"
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120 label="Bowtie2 output on ${on_string} (MetaPhlAn)">
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121 <filter>bowtie2_output != '--no_map' </filter>
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122 </data>
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123
9
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124 <data format="sam" name="sam_output_file"
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125 metadata="input_sequence_file"
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126 label="Sam output on ${on_string} (MetaPhlAn)">
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127 <filter>sam_output</filter>
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128 </data>
9
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129 <data format="biom" name="biom_output_file"
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130 metadata="input_sequence_file"
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131 label="Biom output on ${on_string} (MetaPhlAn)">
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132 <filter>biom_output</filter>
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133 </data>
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134 </outputs>
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135
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136 <tests>
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137 <test>
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138 <param name="input_file" value="input_sequences.fastq"/>
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139 <param name="analysis_type_select" value="rel_ab" />
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140 <param name="taxonomic_level" value="a" />
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141 <param name="min_cu_len" value="2000" />
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142 <param name="min_alignment_len" value="0" />
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143 <param name="ignore_viruses" value="" />
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144 <param name="ignore_eukaryotes" value="" />
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145 <param name="ignore_bacteria" value="" />
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146 <param name="ignore_archaea" value="" />
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147 <param name="stat_q" value="0.1" />
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148 <param name="bowtie2_output" value='--no_map' />
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149 <param name="sam_output" value='False' />
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150 <param name="biom_output" value='False' />
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151 <output name="output_file" file="profiled_metagenome.txt"/>
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152 </test>
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153 </tests>
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154
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155 <help><![CDATA[
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156
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157 **What it does**
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158
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159 MetaPhlAn is a computational tool for profiling the composition of microbial
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160 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun
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161 sequencing data with species level resolution
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162
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163 .. _MetaPhlAn2 user manual: https://bitbucket.org/biobakery/metaphlan2
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164
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165 -----
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166
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167 **Input**
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168
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169 Metaphlan2 takes as input a sequence file in fasta, fastq, a BowTie2 produced
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170 SAM file or an intermediary mapping file of the metagenome generated by a
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171 previous MetaPhlAn
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172
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173 -----
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174
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175 **Parameters**
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176
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177 Several parameters can modulate the MetaPhlAn execution
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178
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179 * Mapping arguments
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180
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181 * Test to avoid saving the output of BowTie2
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182
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183 * Post-mapping arguments
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184
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185 * Taxonomic level for the relative abundance output
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186 * Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances
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187 * Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded
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188 * Tests to avoid profiling of virus, eukaryotes, bacteria and/or archea
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189 * Quantile value
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190
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191 * Additional analysis types and arguments
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192
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193 * Type of analyse to perform and some parameters for specific analysis type
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194
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195 -----
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196
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197 **Outputs**
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198
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199 The main output file is a tab-separated output file of the predicted taxon
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200 relative abundances.
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201
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202 Given the choosen parameters, other output files can be:
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203
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204 * a sam output file
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205 * a biom output fime
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206 * a BowTie2 output file
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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>