Mercurial > repos > iuc > maaslin2
changeset 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 |
| files | maaslin2.xml macros.xml |
| diffstat | 2 files changed, 144 insertions(+), 17 deletions(-) [+] |
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--- a/maaslin2.xml Wed Mar 13 10:32:52 2024 +0000 +++ b/maaslin2.xml Mon Apr 29 10:33:48 2024 +0000 @@ -7,6 +7,34 @@ <expand macro="xrefs"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ + +## get column names of fixed and random effect from the input file, since galaxy +## can only return indices with type="data_column" +## using awk so that the file is only parsed on command line execution + +#if $fixed_effects +#set idx = [] +#for $i in $fixed_effects: + #silent idx.append(f'${i}') +#end for +#set idx_for_awk = ','.join(idx) + +fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` && +echo 'Assigned fixed effects as:' \$fixed_effects && +#end if + + +#if $random_effects +#set idx = [] +#for $i in $random_effects: + #silent idx.append(f'${i}') +#end for +#set idx_for_awk = ','.join(idx) + +random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` && +echo 'Assigned random effects as:' \$random_effects && +#end if + ln -s '$input_data' 'input_data.tsv' && ln -s '$input_metadata' 'input_metadata.tsv' @@ -31,10 +59,10 @@ --analysis_method '$additional_options.analysis_method' #end if #if $random_effects - --random_effects '$random_effects' + --random_effects \$random_effects #end if #if $fixed_effects - --fixed_effects '$fixed_effects' + --fixed_effects \$fixed_effects #end if #if $additional_options.correction --correction '$additional_options.correction' @@ -51,19 +79,17 @@ 'outputFolder' && cd outputFolder && mkdir -p figures/ && cp *.pdf figures + ]]></command> <inputs> <param name="input_data" type="data" format="tabular" label="Data (or features) file"/> <param name="input_metadata" type="data" format="tabular" label="Metadata file"/> - <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"> - <option value="diagnosis" selected="true">diagnosis</option> - <option value="dysbiosisnonIBD" selected="true">dysbiosisnonIBD</option> - <option value="dysbiosisUC" selected="true">dysbiosisUC</option> - <option value="dysbiosisCD" selected="true">dysbiosisCD</option> - <option value="antibiotics" selected="true">antibiotics</option> - <option value="age" selected="true">age</option> - </param> - <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"/> + <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 " /> + + <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" /> + + + <section name="additional_options" title="Additional Options" expanded="true"> <param argument="--min_abundance" type="float" value="0.0" optional="true" label="Minimum abundance" help="The minimum abundance for each feature"/> <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"/> @@ -87,7 +113,11 @@ <option value="NEGBIN">NEGBIN</option> <option value="ZINB">ZINB</option> </param> - <param argument="--correction" type="text" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value"/> + <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing the q-value, Default: BH "> + + <option value="BH">Benjamini-Hochberg(BH)</option> + <option value="BY">Benjamini-Yekutieli(BY)</option> + </param> <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"/> </section> <section name="output" title="Set Plotting Output" expanded="true"> @@ -115,8 +145,8 @@ <test expect_num_outputs="5"> <param name="input_data" value="HMP2_taxonomy.tsv"/> <param name="input_metadata" value="HMP2_metadata.tsv"/> - <param name="random_effects" value="site,subject"/> - <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD,dysbiosisUC,dysbiosisCD,antibiotics,age"/> + <param name="random_effects" value= "2,5"/> + <param name="fixed_effects" value="4,9,10,11,6,3"/> <section name="additional_options"> <param name="min_abundance" value="0.0"/> <param name="min_prevalence" value="0.1"/> @@ -198,7 +228,7 @@ <test expect_num_outputs="5"> <param name="input_data" value="HMP2_taxonomy.tsv"/> <param name="input_metadata" value="HMP2_metadata.tsv"/> - <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/> + <param name="fixed_effects" value="4,9"/> <section name="additional_options"> <param name="min_abundance" value="0.0"/> <param name="min_prevalence" value="0.1"/> @@ -245,7 +275,7 @@ <test expect_num_outputs="5"> <param name="input_data" value="HMP2_taxonomy.tsv"/> <param name="input_metadata" value="HMP2_metadata.tsv"/> - <param name="fixed_effects" value="diagnosis,dysbiosisnonIBD"/> + <param name="fixed_effects" value="4,9"/> <section name="additional_options"> <param name="min_abundance" value="0.0001"/> <param name="min_prevalence" value="0.1"/> @@ -304,6 +334,100 @@ </element> </output_collection> </test> + <test expect_num_outputs="5"> + <param name="input_data" value="HMP2_taxonomy.tsv"/> + <param name="input_metadata" value="HMP2_metadata.tsv"/> + <param name="random_effects" value="3" /> + <section name="additional_options"> + <param name="min_abundance" value="0.0"/> + <param name="min_prevalence" value="0.1"/> + <param name="max_significance" value="0.25"/> + <param name="normalization" value="TSS"/> + <param name="transform" value="LOG"/> + <param name="analysis_method" value="LM"/> + <param name="correction" value="BY"/> + <param name="standardize" value="True"/> + </section> + <section name="output"> + <param name="plot_heatmap" value="true"/> + <param name="heatmap_first_n" value="50"/> + <param name="plot_scatter" value="true"/> + <param name="residuals_output" value="true"/> + </section> + <output name="all_results"> + <assert_contents> + <has_text text="feature"/> + <has_n_lines n="8092"/> + <has_n_columns n="9"/> + </assert_contents> + </output> + <output name="significant_results"> + <assert_contents> + <has_text text="subject"/> + <has_n_lines n="216" delta="5"/> + <has_n_columns n="9"/> + </assert_contents> + </output> + <output name="residuals"> + <assert_contents> + <has_size value="671142" delta="1000"/> + </assert_contents> + </output> + <output_collection name="figures_pdfs" type="list"> + <element name="heatmap.pdf" ftype="pdf"> + <assert_contents> + <has_size value="7000" delta="1000" /> + </assert_contents> + </element> + </output_collection> + </test> + <test expect_num_outputs="5"> + <param name="input_data" value="HMP2_taxonomy.tsv"/> + <param name="input_metadata" value="HMP2_metadata.tsv"/> + + <section name="additional_options"> + <param name="min_abundance" value="0.0"/> + <param name="min_prevalence" value="0.1"/> + <param name="max_significance" value="0.25"/> + <param name="normalization" value="TSS"/> + <param name="transform" value="LOG"/> + <param name="analysis_method" value="LM"/> + <param name="correction" value="BH"/> + <param name="standardize" value="True"/> + </section> + <section name="output"> + <param name="plot_heatmap" value="true"/> + <param name="heatmap_first_n" value="50"/> + <param name="plot_scatter" value="true"/> + <param name="residuals_output" value="true"/> + </section> + <output name="all_results"> + <assert_contents> + <has_text text="feature"/> + <has_n_lines n="8092"/> + <has_n_columns n="9"/> + </assert_contents> + </output> + <output name="significant_results"> + <assert_contents> + <has_text text="subject"/> + <has_n_lines n="880"/> + <has_n_columns n="9"/> + </assert_contents> + </output> + <output name="residuals"> + <assert_contents> + <has_size value="670759" delta="1000"/> + </assert_contents> + </output> + <output_collection name="figures_pdfs" type="list"> + <element name="heatmap.pdf" ftype="pdf"> + <assert_contents> + <has_size value="7900" delta="1000" /> + </assert_contents> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ @HELP_HEADER@ @@ -347,6 +471,9 @@ - It only includes associations with q-values <= to the threshold. - Data frame with residuals for each feature (R data file) - This file contains a data frame with residuals for each feature. + +Correction methods to compute the q-value : https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/p.adjust + 2- Visualization output files - Heatmap of the significant associations (PDF file) - This file contains a heatmap of the significant associations.