Mercurial > repos > iuc > picrust_compare_biom

annotate compare_biom.xml @ 4:8e2ac1b8f70a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 899e24f2aecad79c80667fb6c938dd4573a98820
author iuc
date Fri, 09 Feb 2024 21:41:50 +0000
parents 9168545e09df
children
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9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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1 <tool id="picrust_compare_biom" name="Compare BIOM tables" version="@TOOL_VERSION@.1">
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2 <description>Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
4
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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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 compare_biom.py
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11 -e '$expected'
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12 -o '$outfile'
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13 $not_relative_abundance_scores
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14 $advanced.compare_observations
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15 $advanced.normalize
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16 $advanced.limit_to_observed_observations
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17 $advanced.limit_to_expected_observations
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18 $advanced.shuffle_samples
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19 '$observed'
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20 ]]></command>
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21 <inputs>
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22 <param argument="-o" name="observed" type="data" format="biom1" label="Observed table" help="The observed table of either relative abundance or real counts"/>
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23 <param argument="-e" name="expected" type="data" format="biom1" label="Expected table" help="The expected table of either relative abundance or real counts"/>
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24 <param argument="--not_relative_abundance_scores" type="boolean" truevalue="--not_relative_abundance_scores" falsevalue="" checked="false" label="Real counts instead of relative abundances?"
0
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25 help="Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN"/>
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26 <section name="advanced" title="Advanced parameters" expanded="false">
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27 <param argument="--compare_observations" type="boolean" truevalue="--compare_observations" falsevalue="" checked="false" label="Compare observations"
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28 help="Calculate accuracy values by comparing between observations (instead of between samples)."/>
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29 <param argument="--normalize" type="boolean" truevalue="--normalize" falsevalue="" checked="false" label="Normalize?"
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30 help="Convert both expected and observed tables to relative abundances (instead of observations)."/>
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31 <param argument="--limit_to_observed_observations" type="boolean" truevalue="--limit_to_observed_observations" falsevalue="" checked="false" label="Limit to observed observations?"
0
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32 help="Ignore observations that are not in the observed table."/>
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33 <param argument="--limit_to_expected_observations" type="boolean" truevalue="--limit_to_expected_observations" falsevalue="" checked="false" label="Limit to expected observations?"
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34 help="Ignore observations that are not in the expected table."/>
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35 <param argument="--shuffle_samples" type="boolean" truevalue="--shuffle_samples" falsevalue="" checked="false" label="Shuffle samples?"
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36 help="Shuffle samples ids randomly before measuring accuracy."/>
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37 </section>
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38 </inputs>
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39 <outputs>
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40 <data format="tabular" name="outfile" label="${tool.name} on ${on_string}"/>
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41 </outputs>
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42 <tests>
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43 <test><!-- relative abundance test -->
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44 <param name="observed" value="observed_ra.biom" ftype="biom1"/>
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45 <param name="expected" value="expected_ra.biom" ftype="biom1"/>
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46 <output name="outfile" ftype="tabular">
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47 <assert_contents>
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48 <has_text_matching expression="file\tlabel\taccuracy"/>
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49 <has_text text="sample1"/>
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50 <has_text text="sample3"/>
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51 <has_text text="sample2"/>
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52 <has_n_lines n="4"/>
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53 <has_n_columns n="16"/>
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54 </assert_contents>
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55 </output>
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56 <assert_command>
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57 <not_has_text text="--not_relative_abundance_scores"/>
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58 <not_has_text text="--compare_observations"/>
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59 <not_has_text text="--normalize"/>
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60 <not_has_text text="--limit_to_observed_observations"/>
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61 <not_has_text text="--limit_to_expected_observations"/>
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62 <not_has_text text="--shuffle_samples"/>
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63 </assert_command>
0
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64 </test>
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65 <test><!-- real counts test -->
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66 <param name="observed" value="observed.biom" ftype="biom1"/>
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67 <param name="expected" value="expected.biom" ftype="biom1"/>
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68 <param name="not_relative_abundance_scores" value="true"/>
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69 <output name="outfile" ftype="tabular">
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70 <assert_contents>
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71 <has_text_matching expression="file\tlabel\taccuracy"/>
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72 <has_text text="sample1"/>
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73 <has_text text="sample3"/>
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74 <has_text text="sample2"/>
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75 <has_n_lines n="4"/>
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76 <has_n_columns n="16"/>
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77 </assert_contents>
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78 </output>
3
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79 <assert_command>
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80 <has_text text="--not_relative_abundance_scores"/>
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81 <not_has_text text="--compare_observations"/>
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82 <not_has_text text="--normalize"/>
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83 <not_has_text text="--limit_to_observed_observations"/>
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84 <not_has_text text="--limit_to_expected_observations"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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85 <not_has_text text="--shuffle_samples"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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86 </assert_command>
0
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87 </test>
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88 <test><!-- all other switches test -->
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89 <param name="observed" value="observed.biom" ftype="biom1"/>
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90 <param name="expected" value="expected.biom" ftype="biom1"/>
3
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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91 <param name="not_relative_abundance_scores" value="true"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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92 <section name="advanced">
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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93 <param name="compare_observations" value="true"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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94 <param name="normalize" value="true"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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95 <param name="limit_to_observed_observations" value="true"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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96 <param name="limit_to_expected_observations" value="true"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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97 <param name="shuffle_samples" value="true"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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98 </section>
0
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99 <output name="outfile" ftype="tabular">
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100 <assert_contents>
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101 <has_text_matching expression="file\tlabel\taccuracy"/>
3
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102 <has_text text="K00005"/>
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103 <has_text text="K00004"/>
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104 <has_text text="K00003"/>
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105 <has_n_lines n="6"/>
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106 <has_n_columns n="16"/>
0
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107 </assert_contents>
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108 </output>
3
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109 <assert_command>
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110 <has_text text="--not_relative_abundance_scores"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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111 <has_text text="--compare_observations"/>
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112 <has_text text="--normalize"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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113 <has_text text="--limit_to_observed_observations"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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114 <has_text text="--limit_to_expected_observations"/>
9168545e09df "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit ee7bd710f5194337040a592a5c9069bc3486a68f"
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115 <has_text text="--shuffle_samples"/>
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116 </assert_command>
0
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117 </test>
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118 </tests>
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119 <help>
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120 <![CDATA[
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121 @PICRUST_OVERVIEW@
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122
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123 **Command Documentation**
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124
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125 Compare an observed table to an expected table using either relative abundance or real counts.
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126
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127 **Input files:**
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128
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129 **Observed table:** A table of observed relative abundances or real counts in .biom format.
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130
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131 **Expected table:** The expected table of relative abundances or real counts in .biom format.
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132
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133 **Output file:** Tab delimited file with various accuracy metrics.
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134
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135 **Optional Parameters:**
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136
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137 *compare observations*
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138
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139 Calculate accuracy values by comparing between observations (instead of between samples) [default: False]
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140
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141 *normalize*
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142
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143 Convert both expected and observed tables to relative abundances (instead of observations) [default: False]
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144
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145 *limit to expected observations*
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146
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147 Ignore observations that are not in the expected table[default: False]
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148
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149 *limit to observed observations*
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150
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151 Ignore observations that are not in the observed table[default: False]
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152
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153 *shuffle samples*
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154
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155 Shuffle samples ids randomly before measuring accuracy[default: False]
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156
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157 *not relative abundance scores*
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158
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159 Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN [default: False]
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160
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161 ]]>
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162 </help>
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163 <expand macro="citations"/>
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164 </tool>