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interaction:fixed effects and corrections modified #5928

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Apr 29, 2024
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interaction:fixed effects and corrections modified #5928

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interaction:fixed effects and corrections modified
renu-pal Mar 27, 2024
8fa089e
fixed effects, random effects , corrections methods modified and vers…
renu-pal Apr 17, 2024
bfc500c
maaslin2: test cases added
renu-pal Apr 19, 2024
02ab4b6
maaslin2 : updated fixed and random effects to include just numbers i…
renu-pal Apr 24, 2024
18bb723
Update tools/maaslin2/maaslin2.xml
bgruening Apr 25, 2024
621439a
maaslin2: update correction help
renu-pal Apr 26, 2024
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159 changes: 143 additions & 16 deletions tools/maaslin2/maaslin2.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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 = []
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@renu-pal you said Yh it did a bit, but it's returning the complete list in case of 'random effect " when user does not choose any option
Could you try to fix that here, i.e. add an if statement, that does not choose any columns if no columns are specified by the user - and also add a test for it ...?

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okay, working on that

#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'
Expand All @@ -31,10 +59,10 @@ Maaslin2.R
--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'
Expand All @@ -51,19 +79,17 @@ Maaslin2.R
'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"/>
Expand All @@ -87,7 +113,11 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
<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">
Expand Down Expand Up @@ -115,8 +145,8 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
<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"/>
Expand Down Expand Up @@ -198,7 +228,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
<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"/>
Expand Down Expand Up @@ -245,7 +275,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
<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"/>
Expand Down Expand Up @@ -304,6 +334,100 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
</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@
Expand Down Expand Up @@ -347,6 +471,9 @@ Output
- 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
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If this is called for the correction, why can it only take BH / BY ? Or is this fixed now ?

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Can you check this link.
https://forum.biobakery.org/t/invalid-p-value-correction-options/3321

It seems there was some issue from their end. So I believe if we update the version, it should work but I am not sure if they fixed the bug. Any way to check that ?

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OK good to know, then the wrapper is fine as is, but you can remove this text from the help section (it will confuse the user since the option is not there); and put it back when we update the tool :)

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Okay, will update that


2- Visualization output files
- Heatmap of the significant associations (PDF file)
- This file contains a heatmap of the significant associations.
Expand Down
2 changes: 1 addition & 1 deletion tools/maaslin2/macros.xml
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Expand Up @@ -21,4 +21,4 @@
<yield/>
</requirements>
</xml>
</macros>
</macros>