annotate maaslin2.xml @ 3:43ccbef89f1d draft

planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
author iuc
date Wed, 26 Jun 2024 09:40:13 +0000
parents faacef62bb54
children
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1 <tool id="maaslin2" name="MaAsLin 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Microbiome Multivariable Association with Linear Models</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="edam_ontology"/>
1
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7 <expand macro="xrefs"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
2
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11 ## get column names of fixed and random effect from the input file, since galaxy
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12 ## can only return indices with type="data_column"
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13 ## using awk so that the file is only parsed on command line execution
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15 #if $fixed_effects
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16 #set idx = []
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17 #for $i in $fixed_effects:
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18 #silent idx.append(f'${i}')
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19 #end for
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20 #set idx_for_awk = ','.join(idx)
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22 fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
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23 echo 'Assigned fixed effects as:' \$fixed_effects &&
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24 #end if
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27 #if $random_effects
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28 #set idx = []
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29 #for $i in $random_effects:
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30 #silent idx.append(f'${i}')
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31 #end for
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32 #set idx_for_awk = ','.join(idx)
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34 random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
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35 echo 'Assigned random effects as:' \$random_effects &&
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36 #end if
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37
0
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38 ln -s '$input_data' 'input_data.tsv'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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39 &&
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40 ln -s '$input_metadata' 'input_metadata.tsv'
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41 &&
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42 Maaslin2.R
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43 #if $additional_options.min_abundance
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44 --min_abundance '$additional_options.min_abundance'
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45 #end if
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46 #if $additional_options.min_prevalence
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47 --min_prevalence '$additional_options.min_prevalence'
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48 #end if
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49 #if $additional_options.max_significance
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50 --max_significance '$additional_options.max_significance'
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51 #end if
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52 #if $additional_options.normalization
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53 --normalization '$additional_options.normalization'
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54 #end if
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55 #if $additional_options.transform
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56 --transform '$additional_options.transform'
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57 #end if
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58 #if $additional_options.analysis_method
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59 --analysis_method '$additional_options.analysis_method'
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60 #end if
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61 #if $random_effects
2
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62 --random_effects \$random_effects
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63 #end if
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64 #if $fixed_effects
2
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65 --fixed_effects \$fixed_effects
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66 #end if
3
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67 #if $reference
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68 --reference '$reference'
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69 #end if
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70
0
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71 #if $additional_options.correction
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72 --correction '$additional_options.correction'
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73 #end if
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74 $additional_options.standardize
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75 $output.plot_heatmap
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76 #if $output.heatmap_first_n
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77 --heatmap_first_n '$output.heatmap_first_n'
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78 #end if
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79 $output.plot_scatter
3
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80 --cores 1
0
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81 'input_data.tsv'
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82 'input_metadata.tsv'
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83 'outputFolder'
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84 &&
3
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85 zip -r out.zip outputFolder &&
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86 cd outputFolder &&
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87 mkdir -p figures/ &&
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88 cp *.pdf figures
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89
2
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90
0
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91 ]]></command>
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92 <inputs>
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93 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
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94 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
2
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95 <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects, Default value: All " />
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96 <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects, Default: None" />
3
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97 <param argument="--reference" type="text" label="Reference" help="Reference for a variable with more than two levels provided as a string of 'variable,reference' comma delimited for multiple variables. " />
0
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98 <section name="additional_options" title="Additional Options" expanded="true">
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99 <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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100 <param argument="--min_prevalence" type="float" value="0.1" optional="true" label="Minimum prevalence" help="The minimum percent of samples for which a feature is detected at minimum abundance"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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101 <param argument="--max_significance" type="float" value="0.25" optional="true" label="Maximum significance" help="The q-value threshold for significance"/>
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102 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply">
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103 <option value="TSS" selected="true">TSS</option>
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104 <option value="CLR">CLR</option>
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105 <option value="CSS">CSS</option>
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106 <option value="NONE">NONE</option>
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107 <option value="TMM">TMM</option>
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108 </param>
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109 <param argument="--transform" type="select" optional="true" label="The transform to apply">
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110 <option value="LOG" selected="true">LOG</option>
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111 <option value="LOGIT">LOGIT</option>
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112 <option value="AST">AST</option>
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113 <option value="NONE">NONE</option>
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114 </param>
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115 <param argument="--analysis_method" type="select" optional="true" label="The analysis method to apply">
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116 <option value="LM" selected="true">LM</option>
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117 <option value="CPLM">CPLM</option>
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118 <option value="NEGBIN">NEGBIN</option>
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119 <option value="ZINB">ZINB</option>
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120 </param>
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121 <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value, Default: BH ">
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122 <option value="BH">Benjamini-Hochberg(BH)</option>
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123 <option value="BY">Benjamini-Yekutieli(BY)</option>
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124 <option value="Bonferroni">Bonferroni</option>
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125 <option value="Holm">Holm</option>
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126 <option value="Hochberg">Hochberg</option>
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127 <option value="Hommel">Hommel</option>
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128 </param>
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129 <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="--standardize FALSE" checked="true" label="Apply z-score so continuous metadata are on the same scale"/>
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130 </section>
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131 <section name="output" title="Set Plotting Output" expanded="true">
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132 <param argument="--plot_heatmap" type="boolean" truevalue="--plot_heatmap TRUE" falsevalue="--plot_heatmap FALSE" checked="true" label="Generate a heatmap for the significant associations"/>
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133 <param argument="--heatmap_first_n" type="integer" value="50" optional="true" label="Heatmap plot first N" help="In heatmap, plot top N features with significant associations"/>
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134 <param argument="--plot_scatter" type="boolean" truevalue="--plot_scatter TRUE" falsevalue="--plot_scatter FALSE" checked="true" label="Generate scatter plots for the significant associations"/>
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135 <param name="residuals_output" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Output data frame with residuals for each feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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136 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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137 </inputs>
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138 <outputs>
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139 <data name="archive_output" format="zip" from_work_dir="out.zip" label="${tool.name} on ${on_string}: zip of the complete output" />
0
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140 <data name="all_results" format="tabular" from_work_dir="outputFolder/all_results.tsv" label="All results ordered by increasing q-value"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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141 <data name="significant_results" format="tabular" from_work_dir="outputFolder/significant_results.tsv" label="Q-values smaller than or equal to the threshold"/>
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142 <data name="residuals" format="rdata" from_work_dir="outputFolder/fits/residuals.rds" label="Data frame with residuals for each feature">
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143 <filter>output['residuals_output'] is True</filter>
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144 </data>
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145 <data format="pdf" name="headmap" from_work_dir="outputFolder/figures/heatmap.pdf" label="Heatmap of the significant associations" >
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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146 <filter>output['plot_heatmap'] is True</filter>
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147 </data>
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148 <collection name="figures_pdfs" type="list" label="Plots" >
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149 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputFolder/figures/" format="pdf"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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150 <filter>output['plot_scatter'] is True</filter>
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151 </collection>
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152 </outputs>
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153 <tests>
3
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154 <test expect_num_outputs="6">
0
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155 <param name="input_data" value="HMP2_taxonomy.tsv"/>
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156 <param name="input_metadata" value="HMP2_metadata.tsv"/>
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157 <param name="random_effects" value= "2,5"/>
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158 <param name="fixed_effects" value="4,9,10,11,6,3"/>
3
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159 <param name="reference" value="diagnosis,nonIBD"/>
0
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160 <section name="additional_options">
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161 <param name="min_abundance" value="0.0"/>
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162 <param name="min_prevalence" value="0.1"/>
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163 <param name="max_significance" value="0.25"/>
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164 <param name="normalization" value="NONE"/>
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165 <param name="transform" value="AST"/>
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166 <param name="analysis_method" value="LM"/>
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167 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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168 <param name="standardize" value="false"/>
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169 </section>
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170 <section name="output">
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171 <param name="plot_heatmap" value="true"/>
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172 <param name="heatmap_first_n" value="50"/>
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173 <param name="plot_scatter" value="true"/>
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174 <param name="residuals_output" value="true"/>
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175 </section>
3
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176 <output name="archive_output">
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177 <assert_contents>
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178 <has_size value="15005328" delta="1000000" />
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179 </assert_contents>
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180 </output>
0
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181 <output name="all_results">
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182 <assert_contents>
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183 <has_text text="feature"/>
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184 <has_n_lines n="610"/>
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iuc
parents:
diff changeset
185 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
186 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
187 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
188 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
189 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
190 <has_text text="dysbiosisCD"/>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
191 <has_n_lines n="159" delta="10"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
192 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
193 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
194 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
195 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
196 <assert_contents>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
197 <has_size value="462386" />
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
198 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
199 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
200 <output name="headmap">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
201 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
202 <has_size value="7373" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
203 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
204 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
205 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
206 <element name="heatmap.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
207 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
208 <has_size value="7373" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
209 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
210 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
211 <element name="age.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
212 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
213 <has_size value="407859" delta="100000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
214 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
215 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
216 <element name="antibiotics.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
217 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
218 <has_size value="1590476" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
219 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
220 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
221 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
222 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
223 <has_size value="1407572" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
224 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
225 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
226 <element name="dysbiosisCD.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
227 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
228 <has_size value="2328523" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
229 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
230 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
231 <element name="dysbiosisnonIBD.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
232 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
233 <has_size value="1032602" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
234 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
235 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
236 <element name="dysbiosisUC.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
237 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
238 <has_size value="1037005" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
239 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
240 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
241 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
242 </test>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
243 <test expect_num_outputs="6">
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
244 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
245 <param name="input_metadata" value="HMP2_metadata.tsv"/>
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
246 <param name="fixed_effects" value="4,9"/>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
247 <param name="reference" value="diagnosis,nonIBD"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
248 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
249 <param name="min_abundance" value="0.0"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
250 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
251 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
252 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
253 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
254 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
255 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
256 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
257 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
258 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
259 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
260 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
261 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
262 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
263 </section>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
264 <output name="archive_output">
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
265 <assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
266 <has_size value="12630049" delta="1000000" />
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
267 </assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
268 </output>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
269 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
270 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
271 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
272 <has_n_lines n="262"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
273 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
274 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
275 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
276 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
277 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
278 <has_text text="diagnosis"/>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
279 <has_n_lines n="175" delta="5"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
280 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
281 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
282 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
283 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
284 <assert_contents>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
285 <has_size value="366875"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
286 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
287 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
288 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
289 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
290 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
291 <has_size value="6234127" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
292 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
293 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
294 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
295 </test>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
296 <test expect_num_outputs="6">
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
297 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
298 <param name="input_metadata" value="HMP2_metadata.tsv"/>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
299 <param name="fixed_effects" value="2,4"/>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
300 <param name="reference" value="site,Cedars-Sinai,diagnosis,UC"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
301 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
302 <param name="min_abundance" value="0.0001"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
303 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
304 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
305 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
306 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
307 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
308 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
309 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
310 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
311 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
312 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
313 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
314 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
315 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
316 </section>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
317 <output name="archive_output">
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
318 <assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
319 <has_size value="18278259" delta="1000000" />
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
320 </assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
321 </output>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
322 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
323 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
324 <has_text text="feature"/>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
325 <has_n_lines n="415" delta="10"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
326 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
327 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
328 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
329 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
330 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
331 <has_text text="diagnosis"/>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
332 <has_n_lines n="300" delta="15"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
333 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
334 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
335 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
336 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
337 <assert_contents>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
338 <has_size value="363118"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
339 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
340 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
341 <output name="headmap">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
342 <assert_contents>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
343 <has_size value="7000" delta="1000" />
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
344 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
345 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
346 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
347 <element name="heatmap.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
348 <assert_contents>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
349 <has_size value="7693" delta="100" />
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
350 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
351 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
352 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
353 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
354 <has_size value="6061545" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
355 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
356 </element>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
357
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
358 </output_collection>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
359 </test>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
360 <test expect_num_outputs="6">
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
361 <param name="input_data" value="HMP2_taxonomy.tsv"/>
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
362 <param name="input_metadata" value="HMP2_metadata.tsv"/>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
363 <param name="fixed_effects" value="7,9"/>
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
364 <param name="random_effects" value="3" />
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
365
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
366 <section name="additional_options">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
367 <param name="min_abundance" value="0.0"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
368 <param name="min_prevalence" value="0.1"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
369 <param name="max_significance" value="0.25"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
370 <param name="normalization" value="TSS"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
371 <param name="transform" value="LOG"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
372 <param name="analysis_method" value="LM"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
373 <param name="correction" value="BY"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
374 <param name="standardize" value="True"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
375 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
376 <section name="output">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
377 <param name="plot_heatmap" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
378 <param name="heatmap_first_n" value="50"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
379 <param name="plot_scatter" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
380 <param name="residuals_output" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
381 </section>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
382 <output name="archive_output">
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
383 <assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
384 <has_size value="8567935" delta="1000000" />
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
385 </assert_contents>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
386 </output>
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
387 <output name="all_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
388 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
389 <has_text text="feature"/>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
390 <has_n_lines n="175" delta="10"/>
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
391 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
392 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
393 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
394 <output name="significant_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
395 <assert_contents>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
396 <has_text text="dysbiosisnonIBD"/>
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
397 <has_n_lines n="95" delta="5"/>
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
398 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
399 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
400 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
401 <output name="residuals">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
402 <assert_contents>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
403 <has_size value="434087"/>
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
404 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
405 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
406 <output_collection name="figures_pdfs" type="list">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
407 <element name="heatmap.pdf" ftype="pdf">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
408 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
409 <has_size value="7000" delta="1000" />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
410 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
411 </element>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
412 </output_collection>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
413 </test>
3
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
414
43ccbef89f1d planemo upload for repository https://github.com/biobakery/Maaslin2 commit 62a738f626aee9c8e1f1c5cbd63a59b3390d4ed5
iuc
parents: 2
diff changeset
415
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
416 </tests>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
417 <help><![CDATA[
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
418 @HELP_HEADER@
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
419 MaAsLin 2
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
420 =========
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
421 MaAsLin2 is the next generation of MaAsLin (Microbiome Multivariable Association with Linear Models).
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
422
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
423 Input
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
424 =====
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
425 MaAsLin2 requires two input files:
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
426
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
427 - Data (or features) tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
428 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
429 - Formatted with features as columns and samples as rows.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
430 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
431 - Possible features in this file include taxonomy or genes.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
432 - Metadata tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
433 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
434 - Formatted with features as columns and samples as rows.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
435 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
436 - Possible metadata in this file include gender or age.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
437
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
438 The data file can contain samples not included in the metadata file (along with the reverse case). For both cases, those samples not included in both files will be removed from the analysis. Also the samples do not need to be in the same order in the two files.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
439
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
440 Output
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
441 ======
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
442 1- Data output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
443 - All results ordered by increasing q-value (tabular file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
444 - Full list of associations that pass MaAsLin2's significance threshold, ordered by increasing q-values
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
445 - This includes the same data as the data.frame returned.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
446 - This file contains all results ordered by increasing q-value.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
447 - The first columns are the metadata and feature names.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
448 - The next two columns are the value and coefficient from the model.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
449 - The next column is the standard deviation from the model.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
450 - The N column is the total number of data points.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
451 - The N.not.zero column is the total of non-zero data points.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
452 - The pvalue from the calculation is the second to last column.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
453 - The qvalue is computed with p.adjust with the correction method.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
454 - Q-values smaller than or equal to the threshold (tabular file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
455 - This file is a subset of the results in the first file.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
456 - It only includes associations with q-values <= to the threshold.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
457 - Data frame with residuals for each feature (R data file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
458 - This file contains a data frame with residuals for each feature.
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
459
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
460 Correction methods to compute the q-value : https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/p.adjust
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
461
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
462 2- Visualization output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
463 - Heatmap of the significant associations (PDF file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
464 - This file contains a heatmap of the significant associations.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
465 - A plot for every significant association found (PDF file(s))
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
466 - A plot is generated for each significant association.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
467 - Scatter plots are used for continuous metadata.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
468 - Box plots are for categorical data.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
469 - Data points plotted are after normalization, filtering, and transform.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
470
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
471 ]]></help>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
472 <citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
473 <citation type="doi">10.1101/2021.01.20.427420</citation>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
474 </citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
475 </tool>