Mercurial > repos > frogs > frogs_stat
diff deseq2_preprocess_macros.xml @ 0:6507a8d42a4f draft default tip
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a
| author | frogs |
|---|---|
| date | Wed, 04 Feb 2026 13:16:44 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq2_preprocess_macros.xml Wed Feb 04 13:16:44 2026 +0000 @@ -0,0 +1,107 @@ +<?xml version="1.0"?> +<macros> + <token name="@DESEQ2_ASV_PREPROCESS_CMD_LINE@"> + deseq2_preprocess.py + --analysis-type 'ASV' + --phyloseq-rdata '$phyloseq_rdata' + #if $multiple.correction == 'true' + --var-exp '$var_exp${multiple.model_type}${multiple.conf_factor}' + #else + --var-exp '$var_exp' + #end if + --output-deseq-rdata '$ASV_deseq_rdata' + </token> + + <xml name="deseq2_asv_preprocess_inputs"> + <!-- Files --> + <param argument="--phyloseq-rdata" type="data" format="rdata" label="Phyloseq object (.Rdata)" help="Rdata file generated by the FROGS Stat 'Phyloseq Import data' tool."/> + <!-- Parameters --> + <param argument="--var-exp" type="text" label="Experimental variable" help="Sample metadata variable expected to influence ASV abundances (e.g., Treatment, Environment, Site, etc.)."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <conditional name="multiple"> + <param name="correction" type="select" label="Correct for a confounding factor?" help="If yes, specify an additional sample metadata variable that could affect ASV abundances."> + <option value="true">True</option> + <option value="false" selected="true">False</option> + </param> + <when value="false"/> + <when value="true"> + <param name="conf_factor" type="text" label="Confounding factor" help="Secondary sample metadata variable to account for (e.g., Gender, Batch, Sampling date, etc.)."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <param name="model_type" type="select" multiple="false" label="Model type" help="Choose an additive model (+) if the effects of the two variables are independent, or an interaction model (*) if their effects are expected to depend on each other."> + <option value="+" selected="true">Linear (+)</option> + <option value="*">Interaction (*)</option> + </param> + </when> + </conditional> + </xml> + + <!-- Test --> + <xml name="deseq2_asv_preprocess_test_input"> + <param name="phyloseq_rdata" value="references/16-phylo_import.Rdata" /> + <param name="var_exp" value="EnvType" /> + </xml> + + <xml name="deseq2_asv_preprocess_test_output"> + <output name="ASV_deseq_rdata" count="1" file="references/23-deseq2_preprocess_asv.Rdata" compare="sim_size" delta="100"/> + </xml> + + <token name="@DESEQ2_FUN_PREPROCESS_CMD_LINE@"> + deseq2_preprocess.py + --analysis-type 'FUNCTION' + --input-functions-abund '$input_functions_abund' + --sample-metadata-tsv '$sample_metadata_tsv' + + #if $multiple.correction == 'true' + --var-exp '$var_exp${multiple.model_type}${multiple.conf_factor}' + #else + --var-exp '$var_exp' + #end if + + --output-phyloseq-rdata '$FUN_phyloseq_rdata' + --output-deseq-rdata '$FUN_deseq_rdata' + + + + </token> + + <xml name="deseq2_fun_preprocess_inputs"> + <!-- Files --> + <param argument="--input-functions-abund" type="data" format="tsv,tabular" label="Function abundances file (.tsv) " help="Input file containing predicted function abundances (e.g., 'picrust2_functions: EC_unstrat_abundance.tsv' generated by the FROGS Func 'picrust2_function' tool)."/> + <param argument="--sample-metadata-tsv" type="data" format="tabular,tsv" label="Sample metadata file (.tsv)" help="Tabular file containing metadata describing each sample (e.g., Treatment, Site, Host type, etc.)."/> + <!-- Parameters --> + <param argument="--var-exp" type="text" label="Experimental variable" help="Sample metadata variable expected to influence functional abundances (e.g., Treatment, Environment, Site, etc.)."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <conditional name="multiple"> + <param name="correction" type="select" label="Correct for a confounding factor?" help="If yes, specify an additional sample metadata variable to account for (e.g., Batch, Gender, etc.)."> + <option value="true">True</option> + <option value="false" selected="true">False</option> + </param> + <when value="false"/> + <when value="true"> + <param name="conf_factor" type="text" label="Confounding factor" help="Secondary sample metadata variable to control for (e.g., Gender, Batch, Sampling date, etc.)."> + <expand macro="restricted_sanitizer_validator"/> + </param> + <param name="model_type" type="select" multiple="false" label="Model type" help="Choose an additive model (+) if the effects of both variables are independent, or an interaction model (*) if their effects depend on each other."> + <option value="+" selected="true">Linear (+)</option> + <option value="*">Interaction (*)</option> + </param> + </when> + </conditional> + </xml> + + <!-- Test --> + <xml name="deseq2_fun_preprocess_test_input"> + <param name="sample_metadata_tsv" value="input/sample_metadata.tsv"/> + <param name="input_functions_abund" value="input/frogsfunc_functions_unstrat_EC.tsv" /> + <param name="var_exp" value="EnvType" /> + </xml> + + <xml name="deseq2_fun_preprocess_test_output"> + <!-- Deseq2 is influenced by other intermediate libraries or packages and results are hard to compare --> + <!-- <output name="FUN_deseq_rdata" count="1" file="references/23-deseq2_preprocess_func.Rdata" compare="sim_size" delta="4000"/> --> + <output name="FUN_phyloseq_rdata" count="1" file="references/23-phyloseq_functions.Rdata" compare="sim_size" delta="10"/> + </xml> +</macros>