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comparison decoupler_pseudobulk.xml @ 1:046d8ff974ff draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 45145f380b27c3092e1fa2249adc36d7d6fdf5fe
author ebi-gxa
date Wed, 27 Sep 2023 01:11:32 +0000
parents 59a7f3f83aec
children 130e25d3ce92
comparison
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0:59a7f3f83aec 1:046d8ff974ff
1 <tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy0" profile="20.05"> 1 <tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy1" 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[
72 </inputs> 72 </inputs>
73 <outputs> 73 <outputs>
74 <data name="pbulk_anndata" format="h5ad" label="${tool.name} on ${on_string}: Pseudo-bulk AnnData"> 74 <data name="pbulk_anndata" format="h5ad" label="${tool.name} on ${on_string}: Pseudo-bulk AnnData">
75 <filter>produce_anndata</filter> 75 <filter>produce_anndata</filter>
76 </data> 76 </data>
77 <data name="count_matrix" format="csv" label="${tool.name} on ${on_string}: Count Matrix" from_work_dir="deseq_output_dir/counts_matrix.csv"/> 77 <data name="count_matrix" format="tabular" label="${tool.name} on ${on_string}: Count Matrix" from_work_dir="deseq_output_dir/counts_matrix.tsv"/>
78 <data name="samples_metadata" format="csv" label="${tool.name} on ${on_string}: Samples Metadata (factors file)" from_work_dir="deseq_output_dir/col_metadata.csv"/> 78 <data name="samples_metadata" format="tabular" label="${tool.name} on ${on_string}: Samples Metadata (factors file)" from_work_dir="deseq_output_dir/col_metadata.tsv"/>
79 <data name="genes_metadata" format="csv" label="${tool.name} on ${on_string}: Genes Metadata" from_work_dir="deseq_output_dir/gene_metadata.csv"/> 79 <data name="genes_metadata" format="tabular" label="${tool.name} on ${on_string}: Genes Metadata" from_work_dir="deseq_output_dir/gene_metadata.tsv"/>
80 <data name="plot_output" format="png" label="${tool.name} on ${on_string}: Pseudobulk plot" from_work_dir="plots_output_dir/pseudobulk_samples.png"> 80 <data name="plot_output" format="png" label="${tool.name} on ${on_string}: Pseudobulk plot" from_work_dir="plots_output_dir/pseudobulk_samples.png">
81 <filter>produce_plots</filter> 81 <filter>produce_plots</filter>
82 </data> 82 </data>
83 <data name="filter_by_expr_plot" format="png" label="${tool.name} on ${on_string}: Filter by Expression plot" from_work_dir="plots_output_dir/filter_by_expr.png"> 83 <data name="filter_by_expr_plot" format="png" label="${tool.name} on ${on_string}: Filter by Expression plot" from_work_dir="plots_output_dir/filter_by_expr.png">
84 <filter>produce_plots</filter> 84 <filter>produce_plots</filter>
103 <output name="pbulk_anndata" ftype="h5ad"> 103 <output name="pbulk_anndata" ftype="h5ad">
104 <assert_contents> 104 <assert_contents>
105 <has_h5_keys keys="obs/psbulk_n_cells"/> 105 <has_h5_keys keys="obs/psbulk_n_cells"/>
106 </assert_contents> 106 </assert_contents>
107 </output> 107 </output>
108 <output name="count_matrix" ftype="csv"> 108 <output name="count_matrix" ftype="tabular">
109 <assert_contents> 109 <assert_contents>
110 <has_n_lines n="3620"/> 110 <has_n_lines n="3620"/>
111 <has_n_columns n="8"/>
111 </assert_contents> 112 </assert_contents>
112 </output> 113 </output>
113 <output name="samples_metadata" ftype="csv"> 114 <output name="samples_metadata" ftype="tabular">
114 <assert_contents> 115 <assert_contents>
115 <has_n_lines n="8"/> 116 <has_n_lines n="8"/>
117 <has_n_columns n="3"/>
116 </assert_contents> 118 </assert_contents>
117 </output> 119 </output>
118 <output name="genes_metadata" ftype="csv"> 120 <output name="genes_metadata" ftype="tabular">
119 <assert_contents> 121 <assert_contents>
120 <has_n_lines n="3620"/> 122 <has_n_lines n="3620"/>
123 <has_n_columns n="13"/>
121 </assert_contents> 124 </assert_contents>
122 </output> 125 </output>
123 <output name="plot_output" ftype="png"> 126 <output name="plot_output" ftype="png">
124 <assert_contents> 127 <assert_contents>
125 <has_size value="31853" delta="3000"/> 128 <has_size value="31853" delta="3000"/>
151 - Plot Samples Figsize: Size of the samples plot as a tuple (two arguments). 154 - Plot Samples Figsize: Size of the samples plot as a tuple (two arguments).
152 - Plot Filtering Figsize: Size of the filtering plot as a tuple (two arguments). 155 - Plot Filtering Figsize: Size of the filtering plot as a tuple (two arguments).
153 156
154 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). 157 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).
155 158
159 You can obtain more information about Decoupler pseudobulk at the developers documentation `here <https://decoupler-py.readthedocs.io/en/latest/notebooks/pseudobulk.html>`_ .
160
156 ]]> 161 ]]>
157 </help> 162 </help>
158 <citations> 163 <citations>
159 <citation type="doi">doi.org/10.1093/bioadv/vbac016</citation> 164 <citation type="doi">10.1093/bioadv/vbac016</citation>
160 </citations> 165 </citations>
161 </tool> 166 </tool>