Mercurial > repos > ebi-gxa > score_genes_aucell
diff decoupler_aucell_score.xml @ 0:1e8697931d73 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit c8c39f14eeee6e7a6d097fd0cb9430b12793eb8b
author | ebi-gxa |
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date | Thu, 09 Nov 2023 11:36:08 +0000 |
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children | e024d8280886 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/decoupler_aucell_score.xml Thu Nov 09 11:36:08 2023 +0000 @@ -0,0 +1,137 @@ +<?xml version="1.0"?> +<tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy0" profile="20.05"> + <description> + scores cells using the AUCell method for gene sets. + </description> + <requirements> + <requirement type="package" version="1.4.0">decoupler</requirement> + </requirements> + <command> + python '$__tool_directory__/decoupler_aucell_score.py' + --input_file '$input_file' + #if $gene_lists_source.source == "gmt" + --gmt_file '$gmt_file' + --gene_sets_to_score '$gene_sets_to_score' + #else: + --gene_lists_to_score '$gene_lists_to_score' + --score_names '$score_names' + #end if + --gene_symbols_field '$gene_symbols_field' + $use_raw + #if $write_anndata: + --write_anndata + --output_file anndata_aucell.h5ad + #else: + --output_file anndata_aucell_per_cell.tsv + #end if + </command> + <inputs> + <param name="input_file" type="data" format="h5ad" label="Input AnnData file" /> + <conditional name="gene_lists_source"> + <param name="source" type="select" label="Source of gene lists to score" help="Choose between using a GMT file and specified gene sets or enumerated genes and gene set names."> + <option value="gmt" selected="true">Gene sets from GMT file</option> + <option value="enumerated">Gene sets enumerated manually</option> + </param> + <when value="gmt"> + <param name="gmt_file" type="data" format="txt" label="GMT file with gene sets" /> + <param name="gene_sets_to_score" type="text" label="Gene sets to score within the GMT file" /> + </when> + <when value="enumerated"> + <param name="gene_lists_to_score" type="text" label="Genes to score" /> + <param name="score_names" type="text" label="Score names" /> + </when> + </conditional> + <param name="gene_symbols_field" type="text" label="Gene symbols field" help="The field in the AnnData var table where gene symbols are stored."/> + <param name="use_raw" type="boolean" value="false" truevalue="--use_raw" falsevalue="" label="Use raw data" help="Use RAW data in the AnnData instead of the X matrix."/> + <param name="write_anndata" type="boolean" value="false" truevalue="--write_anndata" falsevalue="" label="Write the modified AnnData object" help="Whether to write or not the same AnnData file again with the signatures on it. If unselected, a text files of cells in rows and signatures in columns (as in Obs) is produced."/> + </inputs> + <outputs> + <data name="output_ad" format="h5ad" from_work_dir="anndata_aucell.h5ad" label="${tool.name} on ${on_string}: Output AnnData file"> + <filter>write_anndata</filter> + </data> + <data name="output_table" format="tabular" from_work_dir="anndata_aucell_per_cell.tsv" label="${tool.name} on ${on_string}: Output AUCell table"> + <filter>not write_anndata</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input_file" value="mito_counted_anndata.h5ad"/> + <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> + <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> + <param name="gene_symbols_field" value="Symbol"/> + <param name="write_anndata" value="true"/> + <conditional name="gene_lists_source"> + <param name="source" value="gmt"/> + </conditional> + <output name="output_ad"> + <assert_contents> + <has_h5_keys keys="obs/AUCell_HALLMARK_NOTCH_SIGNALING"/> + <has_h5_keys keys="obs/AUCell_HALLMARK_APICAL_SURFACE"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_file" value="mito_counted_anndata.h5ad"/> + <param name="gene_lists_to_score" value="Cd8b1,Cd8b2,Cd8a,Cd4,Nrp1,Cd80:Il1a,Il1b,Il6,Nos2,Tlr2,Tlr4,Cd80"/> + <param name="score_names" value="TCell,Macro"/> + <param name="gene_symbols_field" value="Symbol"/> + <param name="write_anndata" value="true"/> + <conditional name="gene_lists_source"> + <param name="source" value="enumerated"/> + </conditional> + <output name="output_ad"> + <assert_contents> + <has_h5_keys keys="obs/AUCell_TCell"/> + <has_h5_keys keys="obs/AUCell_Macro"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="input_file" value="mito_counted_anndata.h5ad"/> + <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> + <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> + <param name="gene_symbols_field" value="Symbol"/> + <param name="write_anndata" value="False"/> + <conditional name="gene_lists_source"> + <param name="source" value="gmt"/> + </conditional> + <output name="output_table"> + <assert_contents> + <has_n_columns n="3"/> + <has_text_matching expression="AUCell_HALLMARK_NOTCH_SIGNALING"/> + </assert_contents> + </output> + </test> + </tests> + <help> +**Description** + +This tool scores cells using the AUCell method for gene sets. + +**Input** + +The input file should be an AnnData object in H5AD format. The tool accepts an H5AD file containing raw or normalized data. + +The tool takes one of two input formats for specifying the gene sets to score: + +1. A GMT file containing gene sets. You can specify which gene sets to use within the GMT file using the "gene_sets_to_score" parameter. +2. A list of genes and their associated score names. You can specify the genes to score using the "gene_lists_to_score" parameter, and their associated score names using the "score_names" parameter. + +In both cases, you must specify the name of the field in the AnnData object that contains the gene symbols using the "gene_symbols_field" parameter. + +You can also specify whether to use the raw data in the AnnData object instead of the X matrix using the "use_raw" parameter. + +**Output** + +The tool outputs an AnnData object containing the scores in the "obs" field, or a tab-separated text file containing the scores for each cell. + +If the "write_anndata" parameter is set to "true", the tool will write the modified AnnData object to an H5AD file. Otherwise, it will output a tab-separated text file containing the scores for each cell. + +**Example** + + + </help> + <citations> + <citation type="doi">10.1093/bioadv/vbac016</citation> + </citations> +</tool> \ No newline at end of file