annotate maaslin2.xml @ 2:faacef62bb54 draft

planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
author iuc
date Mon, 29 Apr 2024 10:33:48 +0000
parents ef2cace85809
children 43ccbef89f1d
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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
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38 ln -s '$input_data' 'input_data.tsv'
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39 &&
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40 ln -s '$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
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62 --random_effects \$random_effects
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63 #end if
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64 #if $fixed_effects
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65 --fixed_effects \$fixed_effects
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66 #end if
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67 #if $additional_options.correction
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68 --correction '$additional_options.correction'
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69 #end if
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70 $additional_options.standardize
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71 $output.plot_heatmap
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72 #if $output.heatmap_first_n
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73 --heatmap_first_n '$output.heatmap_first_n'
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74 #end if
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75 $output.plot_scatter
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76 --cores \${GALAXY_SLOTS:-4}
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77 'input_data.tsv'
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78 'input_metadata.tsv'
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79 'outputFolder'
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80 &&
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81 cd outputFolder && mkdir -p figures/ && cp *.pdf figures
2
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82
0
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83 ]]></command>
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84 <inputs>
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85 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
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86 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
2
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87 <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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88
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89 <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" />
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90
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91
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92
0
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93 <section name="additional_options" title="Additional Options" expanded="true">
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94 <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/>
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95 <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"/>
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96 <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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97 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply">
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98 <option value="TSS" selected="true">TSS</option>
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99 <option value="CLR">CLR</option>
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100 <option value="CSS">CSS</option>
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101 <option value="NONE">NONE</option>
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102 <option value="TMM">TMM</option>
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103 </param>
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104 <param argument="--transform" type="select" optional="true" label="The transform to apply">
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105 <option value="LOG" selected="true">LOG</option>
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106 <option value="LOGIT">LOGIT</option>
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107 <option value="AST">AST</option>
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108 <option value="NONE">NONE</option>
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109 </param>
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110 <param argument="--analysis_method" type="select" optional="true" label="The analysis method to apply">
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111 <option value="LM" selected="true">LM</option>
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112 <option value="CPLM">CPLM</option>
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113 <option value="NEGBIN">NEGBIN</option>
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114 <option value="ZINB">ZINB</option>
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115 </param>
2
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116 <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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117
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118 <option value="BH">Benjamini-Hochberg(BH)</option>
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119 <option value="BY">Benjamini-Yekutieli(BY)</option>
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120 </param>
0
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121 <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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122 </section>
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123 <section name="output" title="Set Plotting Output" expanded="true">
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124 <param argument="--plot_heatmap" type="boolean" truevalue="--plot_heatmap TRUE" falsevalue="--plot_heatmap FALSE" checked="true" label="Generate a heatmap for the significant associations"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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125 <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"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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126 <param argument="--plot_scatter" type="boolean" truevalue="--plot_scatter TRUE" falsevalue="--plot_scatter FALSE" checked="true" label="Generate scatter plots for the significant associations"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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127 <param name="residuals_output" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Output data frame with residuals for each feature"/>
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128 </section>
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129 </inputs>
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130 <outputs>
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131 <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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132 <data name="significant_results" format="tabular" from_work_dir="outputFolder/significant_results.tsv" label="Q-values smaller than or equal to the threshold"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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133 <data name="residuals" format="rdata" from_work_dir="outputFolder/residuals.rds" label="Data frame with residuals for each feature">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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134 <filter>output['residuals_output'] is True</filter>
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135 </data>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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136 <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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137 <filter>output['plot_heatmap'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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diff changeset
138 </data>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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139 <collection name="figures_pdfs" type="list" label="Plots" >
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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140 <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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141 <filter>output['plot_scatter'] is True</filter>
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142 </collection>
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diff changeset
143 </outputs>
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144 <tests>
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145 <test expect_num_outputs="5">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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146 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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147 <param name="input_metadata" value="HMP2_metadata.tsv"/>
2
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148 <param name="random_effects" value= "2,5"/>
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149 <param name="fixed_effects" value="4,9,10,11,6,3"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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150 <section name="additional_options">
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151 <param name="min_abundance" value="0.0"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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152 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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153 <param name="max_significance" value="0.25"/>
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diff changeset
154 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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diff changeset
155 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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156 <param name="analysis_method" value="LM"/>
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diff changeset
157 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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diff changeset
158 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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diff changeset
159 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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160 <section name="output">
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161 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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162 <param name="heatmap_first_n" value="50"/>
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163 <param name="plot_scatter" value="true"/>
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164 <param name="residuals_output" value="true"/>
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165 </section>
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166 <output name="all_results">
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parents:
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167 <assert_contents>
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168 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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169 <has_n_lines n="610"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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170 <has_n_columns n="9"/>
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parents:
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171 </assert_contents>
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172 </output>
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173 <output name="significant_results">
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174 <assert_contents>
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175 <has_text text="dysbiosisCD"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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176 <has_n_lines n="159"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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177 <has_n_columns n="9"/>
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parents:
diff changeset
178 </assert_contents>
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179 </output>
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diff changeset
180 <output name="residuals">
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parents:
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181 <assert_contents>
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182 <has_size value="462746" delta="1000"/>
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parents:
diff changeset
183 </assert_contents>
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parents:
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184 </output>
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parents:
diff changeset
185 <output name="headmap">
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parents:
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186 <assert_contents>
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parents:
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187 <has_size value="7373" delta="1000" />
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iuc
parents:
diff changeset
188 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
189 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
190 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
191 <element name="heatmap.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
192 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
193 <has_size value="7373" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
194 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
195 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
196 <element name="age.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
197 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
198 <has_size value="407859" delta="100000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
199 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
200 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
201 <element name="antibiotics.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
202 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
203 <has_size value="1590476" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
204 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
205 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
206 <element name="diagnosis.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="1407572" delta="1000000" />
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="dysbiosisCD.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="2328523" delta="1000000" />
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="dysbiosisnonIBD.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="1032602" 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="dysbiosisUC.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="1037005" 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 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
227 </test>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
228 <test expect_num_outputs="5">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
229 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
230 <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
231 <param name="fixed_effects" value="4,9"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
232 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
233 <param name="min_abundance" value="0.0"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
234 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
235 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
236 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
237 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
238 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
239 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
240 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
241 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
242 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
243 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
244 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
245 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
246 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
247 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
248 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
249 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
250 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
251 <has_n_lines n="262"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
252 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
253 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
254 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
255 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
256 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
257 <has_text text="diagnosis"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
258 <has_n_lines n="175"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
259 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
260 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
261 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
262 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
263 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
264 <has_size value="367224" delta="1000"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
265 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
266 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
267 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
268 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
269 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
270 <has_size value="6234127" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
271 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
272 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
273 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
274 </test>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
275 <test expect_num_outputs="5">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
276 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
277 <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
278 <param name="fixed_effects" value="4,9"/>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
279 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
280 <param name="min_abundance" value="0.0001"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
281 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
282 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
283 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
284 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
285 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
286 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
287 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
288 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
289 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
290 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
291 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
292 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
293 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
294 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
295 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
296 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
297 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
298 <has_n_lines n="250"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
299 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
300 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
301 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
302 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
303 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
304 <has_text text="diagnosis"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
305 <has_n_lines n="172"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
306 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
307 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
308 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
309 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
310 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
311 <has_size value="359943" delta="1000"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
312 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
313 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
314 <output name="headmap">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
315 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
316 <has_size value="6554" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
317 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
318 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
319 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
320 <element name="heatmap.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
321 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
322 <has_size value="6554" delta="1000" />
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 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
325 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
326 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
327 <has_size value="6061545" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
328 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
329 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
330 <element name="dysbiosisnonIBD.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
331 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
332 <has_size value="2599373" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
333 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
334 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
335 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
336 </test>
2
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
337 <test expect_num_outputs="5">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
338 <param name="input_data" value="HMP2_taxonomy.tsv"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
339 <param name="input_metadata" value="HMP2_metadata.tsv"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
340 <param name="random_effects" value="3" />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
341 <section name="additional_options">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
342 <param name="min_abundance" value="0.0"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
343 <param name="min_prevalence" value="0.1"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
344 <param name="max_significance" value="0.25"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
345 <param name="normalization" value="TSS"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
346 <param name="transform" value="LOG"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
347 <param name="analysis_method" value="LM"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
348 <param name="correction" value="BY"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
349 <param name="standardize" value="True"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
350 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
351 <section name="output">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
352 <param name="plot_heatmap" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
353 <param name="heatmap_first_n" value="50"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
354 <param name="plot_scatter" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
355 <param name="residuals_output" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
356 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
357 <output name="all_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
358 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
359 <has_text text="feature"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
360 <has_n_lines n="8092"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
361 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
362 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
363 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
364 <output name="significant_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
365 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
366 <has_text text="subject"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
367 <has_n_lines n="216" delta="5"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
368 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
369 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
370 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
371 <output name="residuals">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
372 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
373 <has_size value="671142" delta="1000"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
374 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
375 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
376 <output_collection name="figures_pdfs" type="list">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
377 <element name="heatmap.pdf" ftype="pdf">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
378 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
379 <has_size value="7000" delta="1000" />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
380 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
381 </element>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
382 </output_collection>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
383 </test>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
384 <test expect_num_outputs="5">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
385 <param name="input_data" value="HMP2_taxonomy.tsv"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
386 <param name="input_metadata" value="HMP2_metadata.tsv"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
387
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
388 <section name="additional_options">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
389 <param name="min_abundance" value="0.0"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
390 <param name="min_prevalence" value="0.1"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
391 <param name="max_significance" value="0.25"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
392 <param name="normalization" value="TSS"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
393 <param name="transform" value="LOG"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
394 <param name="analysis_method" value="LM"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
395 <param name="correction" value="BH"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
396 <param name="standardize" value="True"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
397 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
398 <section name="output">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
399 <param name="plot_heatmap" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
400 <param name="heatmap_first_n" value="50"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
401 <param name="plot_scatter" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
402 <param name="residuals_output" value="true"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
403 </section>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
404 <output name="all_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
405 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
406 <has_text text="feature"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
407 <has_n_lines n="8092"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
408 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
409 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
410 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
411 <output name="significant_results">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
412 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
413 <has_text text="subject"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
414 <has_n_lines n="880"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
415 <has_n_columns n="9"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
416 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
417 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
418 <output name="residuals">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
419 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
420 <has_size value="670759" delta="1000"/>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
421 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
422 </output>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
423 <output_collection name="figures_pdfs" type="list">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
424 <element name="heatmap.pdf" ftype="pdf">
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
425 <assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
426 <has_size value="7900" delta="1000" />
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
427 </assert_contents>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
428 </element>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
429 </output_collection>
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
430 </test>
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
431 </tests>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
432 <help><![CDATA[
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
433 @HELP_HEADER@
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
434 MaAsLin 2
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
435 =========
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
436 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
437
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
438 Input
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 MaAsLin2 requires two input files:
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 - Data (or features) tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
443 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
444 - 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
445 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
446 - 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
447 - Metadata tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
448 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
449 - 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
450 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
451 - 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
452
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
453 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
454
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
455 Output
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
456 ======
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
457 1- Data output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
458 - 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
459 - 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
460 - 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
461 - 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
462 - 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
463 - 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
464 - 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
465 - 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
466 - 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
467 - 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
468 - 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
469 - 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
470 - 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
471 - 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
472 - 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
473 - 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
474
faacef62bb54 planemo upload for repository https://github.com/biobakery/Maaslin2 commit c6827285ea113de141b6f4111cffe872b6e2cef3
iuc
parents: 1
diff changeset
475 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
476
0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
477 2- Visualization output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
478 - Heatmap of the significant associations (PDF file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
479 - 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
480 - 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
481 - A plot is generated for each significant association.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
482 - Scatter plots are used for continuous metadata.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
483 - Box plots are for categorical data.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
484 - Data points plotted are after normalization, filtering, and transform.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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485
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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486 ]]></help>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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487 <citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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488 <citation type="doi">10.1101/2021.01.20.427420</citation>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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489 </citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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490 </tool>