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1 <tool id="export2graphlan" name="export2graphlan" version="1.0.0">
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2 <description>Export to Graphlan</description>
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3 <command interpreter="python">
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4 export2graphlan.py
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5 -i $inp_data
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6 -o $out_data
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7 -t $output_tree_file
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8 -a $output_annot_file
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18
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9
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10 --annotations $export_annotations
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11 --external_annotations $export_external_annotations
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14
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12 --background_levels $background_levels
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17
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13 #if $str($background_clades) != " ":
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16
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14 --background_clades $background_clades
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15 #end if
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18
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16 #if $str($background_colors) != " ":
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17 --background_colors $background_colors
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18 #end if
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19 #if $str($export_title) != " ":
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20 --title $export_title
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21 #end if
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22 --title_font_size $title_font_size
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23 --def_clade_size $def_clade_size
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24 --min_clade_size $min_clade_size
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25 --max_clade_size $max_clade_size
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20
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26 --def_font_size $def_font_size
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27 --min_font_size $min_font_size
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28 --max_font_size $max_font_size
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29 --annotation_legend_font_size $annotation_legend_font_size
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30 --abundance_threshold $abundance_threshold
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21
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31 #if $most_abundant > 0:
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32 --most_abundant $most_abundant
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33 #end if
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34 --skip_rows 1,2
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35 </command>
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36
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37 <inputs>
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19
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38 <param format="tabular" name="inp_data" type="data" label="Input used to run Lefse" help="This is the file that was used as input for Lefse"/>
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39 <param format="lefse_internal_res" name="out_data" type="data" label="Output of Lefse" help="This is the Lefse output file"/>
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40 <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
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41 <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>
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42 <param name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/>
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43 <param name="background_clades" type="text" format="text" label="Background Clades" value=" " />
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44 <param name="background_colors" type="text" format="text" label="Background Colors" value=" " />
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45 <param name="export_title" type="text" format="text" label="Title" value=" "/>
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46 <param name="title_font_size" type="integer" size="4" value="15" label="Title font size"/>
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47 <param name="def_clade_size" type="integer" size="4" value="0" label="Default Clade size"/>
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48 <param name="min_clade_size" type="integer" size="4" value="20" label="Minimum Clade size that are Biomarkers"/>
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49 <param name="max_clade_size" type="integer" size="4" value="200" label="Maximum Clade size that are Biomarkers"/>
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50 <param name="def_font_size" type="integer" size="4" value="10" label="Default font size"/>
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51 <param name="min_font_size" type="integer" size="4" value="8" label="Minimum font size "/>
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52 <param name="max_font_size" type="integer" size="4" value="12" label="Maximum font size "/>
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53 <param name="annotation_legend_font_size" type="integer" size="4" value="10" label="Annotation legend font size "/>
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54 <param name="abundance_threshold" type="float" value="20.0" label="Abundance threshold: minimun abundace value for a clade to be annotated"/>
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55 <param name="most_abundant" type="integer" size="4" value="0" label=" When only lefse_input is provided, you can specify how many clades to highlight "/>
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56
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57 least_biomarkers
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58 </inputs>
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59 <outputs>
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60 <data name="output_annot_file" format="circl" />
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61 <data name="output_tree_file" format="circl" />
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62 </outputs>
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63
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64 <help>
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65 Overview
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66 ========
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67 **export2graphlan** is an *OPTIONAL* tool that automatically convert **LEfSe**, **MetaPhlAn2**, and **HUMAnN** input and/or output files, to **GraPhlAn**. Input file can be also given in BIOM (both 1 and 2) format.
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68
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69 The aim of this tool is to support biologists, helping them by provide the tree and the annotation file for GraPhlAn, automatically.
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70
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71 Input files
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72 -----------
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73
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74 As shown in the image below, export2graphlan can work with just one of the following files or with both of them.
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75
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76 * **Result of MetaPhlAn or HUMAnN analysis**: As depicted in the image below, this file can be the result of a MetaPhlAn analysis or a HUMAnN analysis. Generally, it is a tab separated file that have for each row a taxonomy and an abundance value.
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77
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78 * **Output of LEfSe**: This file is the result of LEfSe execute on the *Result of MetaPhlAn or HUMAnN analysis* file. This file allow GraPhlAn to highlight for you the found biomarkers.
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79
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80 Input parameters
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81 ----------------
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82
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83 --annotations ANNOTATIONS
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84 List which levels should be annotated in the tree. Use
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85 a comma separate values form, e.g.,
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86 --annotation_levels 1,2,3. Default is None
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87 --external_annotations EXTERNAL_ANNOTATIONS
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88 List which levels should use the external legend for
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89 the annotation. Use a comma separate values form,
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90 e.g., --annotation_levels 1,2,3. Default is None
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91 --background_levels BACKGROUND_LEVELS
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92 List which levels should be highlight with a shaded
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93 background. Use a comma separate values form, e.g.,
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94 --background_levels 1,2,3
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95 --background_clades BACKGROUND_CLADES
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96 Specify the clades that should be highlight with a
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97 shaded background. Use a comma separate values form
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98 and surround the string with " if it contains spaces.
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99 Example: --background_clades "Bacteria.Actinobacteria,
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100 Bacteria.Bacteroidetes.Bacteroidia,
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101 Bacteria.Firmicutes.Clostridia.Clostridiales"
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102 --background_colors BACKGROUND_COLORS
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103 Set the color to use for the shaded background. Colors
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104 can be either in RGB or HSV (using a semi-colon to
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105 separate values, surrounded with ()) format. Use a
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106 comma separate values form and surround the string
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107 with " if it contains spaces. Example:
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108 --background_colors "#29cc36, (150; 100; 100), (280;
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109 80; 88)"
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110 --title TITLE If specified set the title of the GraPhlAn plot.
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111 Surround the string with " if it contains spaces,
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112 e.g., --title "Title example"
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113 --title_font_size TITLE_FONT_SIZE
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114 Set the title font size. Default is 15
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115 --def_clade_size DEF_CLADE_SIZE
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116 Set a default size for clades that are not found as
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117 biomarkers by LEfSe. Default is 10
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118 --min_clade_size MIN_CLADE_SIZE
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119 Set the minimum value of clades that are biomarkers.
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120 Default is 20
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121 --max_clade_size MAX_CLADE_SIZE
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122 Set the maximum value of clades that are biomarkers.
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123 Default is 200
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124 --def_font_size DEF_FONT_SIZE
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125 Set a default font size. Default is 10
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126 --min_font_size MIN_FONT_SIZE
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127 Set the minimum font size to use. Default is 8
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128 --max_font_size MAX_FONT_SIZE
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129 Set the maximum font size. Default is 12
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130 --annotation_legend_font_size ANNOTATION_LEGEND_FONT_SIZE
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131 Set the font size for the annotation legend. Default
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132 is 10
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133 --abundance_threshold ABUNDANCE_THRESHOLD
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134 Set the minimun abundace value for a clade to be
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135 annotated. Default is 20.0
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136 --most_abundant MOST_ABUNDANT
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137 When only lefse_input is provided, you can specify how
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138 many clades highlight. Since the biomarkers are
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139 missing, they will be chosen from the most abundant
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140 --least_biomarkers LEAST_BIOMARKERS
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141 When only lefse_input is provided, you can specify the
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142 minimum number of biomarkers to extract. The taxonomy
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143 is parsed, and the level is choosen in order to have
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144 at least the specified number of biomarkers
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145 --discard_otus If specified the OTU ids will be discarde from the
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146 taxonmy. Default behavior keep OTU ids in taxonomy
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147 --internal_levels If specified sum-up from leaf to root the abundances
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148 values. Default behavior do not sum-up abundances on
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149 the internal nodes
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150
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151 input parameters:
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152
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153 -i LEFSE_INPUT, --lefse_input LEFSE_INPUT
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154
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155 -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT
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156
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157 output parameters:
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158
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159 -t TREE, --tree TREE Output filename where save the input tree for GraPhlAn
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160
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161 -a ANNOTATION, --annotation ANNOTATION : This is the Output filename where to save GraPhlAn annotation
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162
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163 Input data matrix parameters:
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164 --sep SEP
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165 --out_table OUT_TABLE : This is where to write the processed data matrix to file
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166
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167 --fname_row FNAME_ROW : Row number containing the names of the features (default 0, specify -1 if no names are present in the matrix)
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168
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169 --sname_row SNAME_ROW
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170 column number containing the names of the samples (default 0, specify -1 if no names are present in the matrix)
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171 --metadata_rows METADATA_ROWS
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172 Row numbers to use as metadata[default None, meaning
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173 no metadata
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174 --skip_rows SKIP_ROWS
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175 Row numbers to skip (0-indexed, comma separated) from
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176 the input file[default None, meaning no rows skipped
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177 --sperc SPERC Percentile of sample value distribution for sample
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178 selection
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179 --fperc FPERC Percentile of feature value distribution for sample
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180 selection
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181 --stop STOP Number of top samples to select (ordering based on
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182 percentile specified by --sperc)
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183 --ftop FTOP Number of top features to select (ordering based on
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184 percentile specified by --fperc)
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185 --def_na DEF_NA Set the default value for missing values [default None
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186 which means no replacement]
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187
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188 Integration
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189 ===========
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190
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191 A graphical representation of how **export2graphlan** can be integrated in the analysis pipeline:
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192
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193 .. image:: https://bitbucket.org/repo/oL6bEG/images/3364692296-graphlan_integration.png
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194 :height: 672
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195 :width: 800
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196
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197 Want to know more?
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198 ==================
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199
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200 If you want to know more about **export2graphlan** please have a look at the tutorial
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201 </help>
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202 </tool>
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