Mercurial > repos > ebi-gxa > decoupler_pseudobulk

comparison decoupler_pseudobulk.xml @ 17:2557d7869e78 draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 626c1018b662202de10ce77f123fc27f584beb9c
author ebi-gxa
date Fri, 13 Jun 2025 09:08:00 +0000
parents 508a93e34599
children
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16:508a93e34599 17:2557d7869e78
1 <tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy9" profile="20.05"> 1 <tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy10" profile="20.05">
2 <description>aggregates single cell RNA-seq data for running bulk RNA-seq methods</description> 2 <description>aggregates single cell RNA-seq data for running bulk RNA-seq methods</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.4.0">decoupler</requirement> 4 <requirement type="package" version="1.4.0">decoupler</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
243 <param name="contrasts_file" value="test_contrasts.txt" ftype="txt"/> 243 <param name="contrasts_file" value="test_contrasts.txt" ftype="txt"/>
244 <param name="min_cells_perc_per_contrast_cond" value="25"/> 244 <param name="min_cells_perc_per_contrast_cond" value="25"/>
245 <param name="adata_obs_fields_to_merge" value="batch,sex:batch,genotype"/> 245 <param name="adata_obs_fields_to_merge" value="batch,sex:batch,genotype"/>
246 <param name="groupby" value="batch_sex"/> 246 <param name="groupby" value="batch_sex"/>
247 <param name="sample_key" value="genotype"/> 247 <param name="sample_key" value="genotype"/>
248 <param name="factor_fields" value="genotype,batch_sex"/> 248 <param name="factor_fields" value="genotype,batch_sex,psbulk_n_cells"/>
249 <param name="mode" value="sum"/> 249 <param name="mode" value="sum"/>
250 <param name="min_cells" value="10"/> 250 <param name="min_cells" value="10"/>
251 <param name="produce_plots" value="true"/> 251 <param name="produce_plots" value="true"/>
252 <param name="produce_anndata" value="true"/> 252 <param name="produce_anndata" value="true"/>
253 <param name="min_counts" value="10"/> 253 <param name="min_counts" value="10"/>
270 </assert_contents> 270 </assert_contents>
271 </output> 271 </output>
272 <output name="samples_metadata" ftype="tabular"> 272 <output name="samples_metadata" ftype="tabular">
273 <assert_contents> 273 <assert_contents>
274 <has_n_lines n="22"/> 274 <has_n_lines n="22"/>
275 <has_n_columns n="3"/> 275 <has_n_columns n="4"/>
276 </assert_contents> 276 </assert_contents>
277 </output> 277 </output>
278 <output name="genes_metadata" ftype="tabular"> 278 <output name="genes_metadata" ftype="tabular">
279 <assert_contents> 279 <assert_contents>
280 <has_n_lines n="3620"/> 280 <has_n_lines n="3620"/>
322 322
323 The tool will output the filtered AnnData, count matrix, samples metadata, genes metadata (in DESeq2 format), and the pseudobulk plot and filter by expression plot (if enabled). Files for filtering genes later on are also generated (to ignore after the DE model). 323 The tool will output the filtered AnnData, count matrix, samples metadata, genes metadata (in DESeq2 format), and the pseudobulk plot and filter by expression plot (if enabled). Files for filtering genes later on are also generated (to ignore after the DE model).
324 324
325 You can obtain more information about Decoupler pseudobulk at the developers documentation `here <https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html>`_ . 325 You can obtain more information about Decoupler pseudobulk at the developers documentation `here <https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html>`_ .
326 326
327 1.4.0+galaxy10: Fixes ability to pass psbulk metadata fields downstream.
328
327 ]]> 329 ]]>
328 </help> 330 </help>
329 <citations> 331 <citations>
330 <citation type="doi">10.1093/bioadv/vbac016</citation> 332 <citation type="doi">10.1093/bioadv/vbac016</citation>
331 </citations> 333 </citations>