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annotate maaslin2.xml @ 0:c629e6de3c49 draft

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"planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
author iuc
date Fri, 05 Nov 2021 11:24:33 +0000
parents
children ef2cace85809
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0
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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1 <tool id="maaslin2" name="MaAsLin 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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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"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$input_data' 'input_data.tsv'
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10 &&
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11 ln -s '$input_metadata' 'input_metadata.tsv'
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12 &&
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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13 Maaslin2.R
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14 #if $additional_options.min_abundance
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15 --min_abundance '$additional_options.min_abundance'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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16 #end if
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17 #if $additional_options.min_prevalence
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18 --min_prevalence '$additional_options.min_prevalence'
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19 #end if
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20 #if $additional_options.max_significance
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21 --max_significance '$additional_options.max_significance'
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22 #end if
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23 #if $additional_options.normalization
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24 --normalization '$additional_options.normalization'
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25 #end if
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26 #if $additional_options.transform
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27 --transform '$additional_options.transform'
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28 #end if
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29 #if $additional_options.analysis_method
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30 --analysis_method '$additional_options.analysis_method'
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31 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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32 #if $random_effects
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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33 --random_effects '$random_effects'
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34 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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35 #if $fixed_effects
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36 --fixed_effects '$fixed_effects'
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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37 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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38 #if $additional_options.correction
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39 --correction '$additional_options.correction'
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40 #end if
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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41 $additional_options.standardize
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42 $output.plot_heatmap
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43 #if $output.heatmap_first_n
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44 --heatmap_first_n '$output.heatmap_first_n'
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45 #end if
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46 $output.plot_scatter
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47 --cores \${GALAXY_SLOTS:-4}
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48 'input_data.tsv'
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49 'input_metadata.tsv'
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50 'outputFolder'
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51 &&
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52 cd outputFolder && mkdir -p figures/ && cp *.pdf figures
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53 ]]></command>
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54 <inputs>
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55 <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
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56 <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
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57 <param argument="--fixed_effects" type="select" multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects">
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58 <option value="diagnosis" selected="true">diagnosis</option>
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59 <option value="dysbiosisnonIBD" selected="true">dysbiosisnonIBD</option>
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60 <option value="dysbiosisUC" selected="true">dysbiosisUC</option>
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61 <option value="dysbiosisCD" selected="true">dysbiosisCD</option>
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62 <option value="antibiotics" selected="true">antibiotics</option>
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63 <option value="age" selected="true">age</option>
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64 </param>
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65 <param argument="--random_effects" type="text" multiple="true" optional="true" label="Random effects" help="The random effects for the model, comma-delimited for multiple effects"/>
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66 <section name="additional_options" title="Additional Options" expanded="true">
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67 <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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68 <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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69 <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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70 <param argument="--normalization" type="select" optional="true" label="The normalization method to apply">
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71 <option value="TSS" selected="true">TSS</option>
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72 <option value="CLR">CLR</option>
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73 <option value="CSS">CSS</option>
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74 <option value="NONE">NONE</option>
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75 <option value="TMM">TMM</option>
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76 </param>
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77 <param argument="--transform" type="select" optional="true" label="The transform to apply">
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78 <option value="LOG" selected="true">LOG</option>
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79 <option value="LOGIT">LOGIT</option>
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80 <option value="AST">AST</option>
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81 <option value="NONE">NONE</option>
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82 </param>
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83 <param argument="--analysis_method" type="select" optional="true" label="The analysis method to apply">
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84 <option value="LM" selected="true">LM</option>
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85 <option value="CPLM">CPLM</option>
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86 <option value="NEGBIN">NEGBIN</option>
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87 <option value="ZINB">ZINB</option>
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88 </param>
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89 <param argument="--correction" type="text" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value"/>
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90 <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"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
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91 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
92 <section name="output" title="Set Plotting Output" expanded="true">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
93 <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"
iuc
parents:
diff changeset
94 <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"
iuc
parents:
diff changeset
95 <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"
iuc
parents:
diff changeset
96 <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"
iuc
parents:
diff changeset
97 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
98 </inputs>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
99 <outputs>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
100 <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"
iuc
parents:
diff changeset
101 <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"
iuc
parents:
diff changeset
102 <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"
iuc
parents:
diff changeset
103 <filter>output['residuals_output'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
104 </data>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
105 <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"
iuc
parents:
diff changeset
106 <filter>output['plot_heatmap'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
107 </data>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
108 <collection name="figures_pdfs" type="list" label="Plots" >
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
109 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputFolder/figures/" format="pdf"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
110 <filter>output['plot_scatter'] is True</filter>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
111 </collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
112 </outputs>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
113 <tests>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
114 <test expect_num_outputs="5">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
115 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
116 <param name="input_metadata" value="HMP2_metadata.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
117 <param name="random_effects" value="site,subject"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
118 <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
119 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
120 <param name="min_abundance" value="0.0"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
121 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
122 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
123 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
124 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
125 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
126 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
127 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
128 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
129 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
130 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
131 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
132 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
133 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
134 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
135 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
136 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
137 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
138 <has_n_lines n="610"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
139 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
140 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
141 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
142 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
143 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
144 <has_text text="dysbiosisCD"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
145 <has_n_lines n="159"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
146 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
147 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
148 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
149 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
150 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
151 <has_size value="462746" delta="1000"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
152 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
153 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
154 <output name="headmap">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
155 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
156 <has_size value="7373" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
157 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
158 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
159 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
160 <element name="heatmap.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
161 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
162 <has_size value="7373" delta="1000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
163 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
164 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
165 <element name="age.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
166 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
167 <has_size value="407859" delta="100000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
168 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
169 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
170 <element name="antibiotics.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
171 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
172 <has_size value="1590476" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
173 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
174 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
175 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
176 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
177 <has_size value="1407572" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
178 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
179 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
180 <element name="dysbiosisCD.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
181 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
182 <has_size value="2328523" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
183 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
184 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
185 <element name="dysbiosisnonIBD.pdf" ftype="pdf">
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 <has_size value="1032602" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
188 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
189 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
190 <element name="dysbiosisUC.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
191 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
192 <has_size value="1037005" delta="1000000" />
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 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
195 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
196 </test>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
197 <test expect_num_outputs="5">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
198 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
199 <param name="input_metadata" value="HMP2_metadata.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
200 <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
201 <section name="additional_options">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
202 <param name="min_abundance" value="0.0"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
203 <param name="min_prevalence" value="0.1"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
204 <param name="max_significance" value="0.25"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
205 <param name="normalization" value="NONE"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
206 <param name="transform" value="AST"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
207 <param name="analysis_method" value="LM"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
208 <param name="correction" value="BH"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
209 <param name="standardize" value="false"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
210 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
211 <section name="output">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
212 <param name="plot_heatmap" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
213 <param name="heatmap_first_n" value="50"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
214 <param name="plot_scatter" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
215 <param name="residuals_output" value="true"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
216 </section>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
217 <output name="all_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
218 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
219 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
220 <has_n_lines n="262"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
221 <has_n_columns n="9"/>
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 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
224 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
225 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
226 <has_text text="diagnosis"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
227 <has_n_lines n="175"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
228 <has_n_columns n="9"/>
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 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
231 <output name="residuals">
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="367224" delta="1000"/>
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 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
236 <output_collection name="figures_pdfs" type="list">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
237 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
238 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
239 <has_size value="6234127" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
240 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
241 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
242 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
243 </test>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
244 <test expect_num_outputs="5">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
245 <param name="input_data" value="HMP2_taxonomy.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
246 <param name="input_metadata" value="HMP2_metadata.tsv"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
247 <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/>
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="0.0001"/>
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>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
264 <output name="all_results">
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 <has_text text="feature"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
267 <has_n_lines n="250"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
268 <has_n_columns n="9"/>
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 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
271 <output name="significant_results">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
272 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
273 <has_text text="diagnosis"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
274 <has_n_lines n="172"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
275 <has_n_columns n="9"/>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
276 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
277 </output>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
278 <output name="residuals">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
279 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
280 <has_size value="359943" delta="1000"/>
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="headmap">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
284 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
285 <has_size value="6554" delta="1000" />
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="heatmap.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="6554" delta="1000" />
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 <element name="diagnosis.pdf" ftype="pdf">
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
295 <assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
296 <has_size value="6061545" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
297 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
298 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
299 <element name="dysbiosisnonIBD.pdf" ftype="pdf">
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 <has_size value="2599373" delta="1000000" />
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
302 </assert_contents>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
303 </element>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
304 </output_collection>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
305 </test>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
306 </tests>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
307 <help><![CDATA[
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
308 @HELP_HEADER@
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
309 MaAsLin 2
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
310 =========
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
311 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
312
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
313 Input
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
314 =====
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
315 MaAsLin2 requires two input files:
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
316
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
317 - Data (or features) tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
318 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
319 - 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
320 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
321 - 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
322 - Metadata tabular file
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
323 - This file is tab-delimited.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
324 - 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
325 - The transpose of this format is also okay.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
326 - 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
327
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
328 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
329
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
330 Output
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
331 ======
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
332 1- Data output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
333 - 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
334 - 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
335 - 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
336 - 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
337 - 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
338 - 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
339 - 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
340 - 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
341 - 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
342 - 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
343 - 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
344 - 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
345 - 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
346 - 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
347 - 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
348 - This file contains a data frame with residuals for each feature.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
349 2- Visualization output files
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
350 - Heatmap of the significant associations (PDF file)
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
351 - 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
352 - 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
353 - A plot is generated for each significant association.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
354 - Scatter plots are used for continuous metadata.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
355 - Box plots are for categorical data.
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
356 - 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
357
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
358 ]]></help>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
359 <citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
360 <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
361 </citations>
c629e6de3c49 "planemo upload for repository https://github.com/biobakery/Maaslin2 commit a0d2ac51212781be1ba2ecd02f0388f6f01cba28"
iuc
parents:
diff changeset
362 </tool>