Mercurial > repos > ebi-gxa > score_genes_aucell
comparison 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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1 <?xml version="1.0"?> | |
2 <tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy0" profile="20.05"> | |
3 <description> | |
4 scores cells using the AUCell method for gene sets. | |
5 </description> | |
6 <requirements> | |
7 <requirement type="package" version="1.4.0">decoupler</requirement> | |
8 </requirements> | |
9 <command> | |
10 python '$__tool_directory__/decoupler_aucell_score.py' | |
11 --input_file '$input_file' | |
12 #if $gene_lists_source.source == "gmt" | |
13 --gmt_file '$gmt_file' | |
14 --gene_sets_to_score '$gene_sets_to_score' | |
15 #else: | |
16 --gene_lists_to_score '$gene_lists_to_score' | |
17 --score_names '$score_names' | |
18 #end if | |
19 --gene_symbols_field '$gene_symbols_field' | |
20 $use_raw | |
21 #if $write_anndata: | |
22 --write_anndata | |
23 --output_file anndata_aucell.h5ad | |
24 #else: | |
25 --output_file anndata_aucell_per_cell.tsv | |
26 #end if | |
27 </command> | |
28 <inputs> | |
29 <param name="input_file" type="data" format="h5ad" label="Input AnnData file" /> | |
30 <conditional name="gene_lists_source"> | |
31 <param name="source" type="select" label="Source of gene lists to score" help="Choose between using a GMT file and specified gene sets or enumerated genes and gene set names."> | |
32 <option value="gmt" selected="true">Gene sets from GMT file</option> | |
33 <option value="enumerated">Gene sets enumerated manually</option> | |
34 </param> | |
35 <when value="gmt"> | |
36 <param name="gmt_file" type="data" format="txt" label="GMT file with gene sets" /> | |
37 <param name="gene_sets_to_score" type="text" label="Gene sets to score within the GMT file" /> | |
38 </when> | |
39 <when value="enumerated"> | |
40 <param name="gene_lists_to_score" type="text" label="Genes to score" /> | |
41 <param name="score_names" type="text" label="Score names" /> | |
42 </when> | |
43 </conditional> | |
44 <param name="gene_symbols_field" type="text" label="Gene symbols field" help="The field in the AnnData var table where gene symbols are stored."/> | |
45 <param name="use_raw" type="boolean" value="false" truevalue="--use_raw" falsevalue="" label="Use raw data" help="Use RAW data in the AnnData instead of the X matrix."/> | |
46 <param name="write_anndata" type="boolean" value="false" truevalue="--write_anndata" falsevalue="" label="Write the modified AnnData object" help="Whether to write or not the same AnnData file again with the signatures on it. If unselected, a text files of cells in rows and signatures in columns (as in Obs) is produced."/> | |
47 </inputs> | |
48 <outputs> | |
49 <data name="output_ad" format="h5ad" from_work_dir="anndata_aucell.h5ad" label="${tool.name} on ${on_string}: Output AnnData file"> | |
50 <filter>write_anndata</filter> | |
51 </data> | |
52 <data name="output_table" format="tabular" from_work_dir="anndata_aucell_per_cell.tsv" label="${tool.name} on ${on_string}: Output AUCell table"> | |
53 <filter>not write_anndata</filter> | |
54 </data> | |
55 </outputs> | |
56 <tests> | |
57 <test expect_num_outputs="1"> | |
58 <param name="input_file" value="mito_counted_anndata.h5ad"/> | |
59 <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> | |
60 <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> | |
61 <param name="gene_symbols_field" value="Symbol"/> | |
62 <param name="write_anndata" value="true"/> | |
63 <conditional name="gene_lists_source"> | |
64 <param name="source" value="gmt"/> | |
65 </conditional> | |
66 <output name="output_ad"> | |
67 <assert_contents> | |
68 <has_h5_keys keys="obs/AUCell_HALLMARK_NOTCH_SIGNALING"/> | |
69 <has_h5_keys keys="obs/AUCell_HALLMARK_APICAL_SURFACE"/> | |
70 </assert_contents> | |
71 </output> | |
72 </test> | |
73 <test expect_num_outputs="1"> | |
74 <param name="input_file" value="mito_counted_anndata.h5ad"/> | |
75 <param name="gene_lists_to_score" value="Cd8b1,Cd8b2,Cd8a,Cd4,Nrp1,Cd80:Il1a,Il1b,Il6,Nos2,Tlr2,Tlr4,Cd80"/> | |
76 <param name="score_names" value="TCell,Macro"/> | |
77 <param name="gene_symbols_field" value="Symbol"/> | |
78 <param name="write_anndata" value="true"/> | |
79 <conditional name="gene_lists_source"> | |
80 <param name="source" value="enumerated"/> | |
81 </conditional> | |
82 <output name="output_ad"> | |
83 <assert_contents> | |
84 <has_h5_keys keys="obs/AUCell_TCell"/> | |
85 <has_h5_keys keys="obs/AUCell_Macro"/> | |
86 </assert_contents> | |
87 </output> | |
88 </test> | |
89 <test expect_num_outputs="1"> | |
90 <param name="input_file" value="mito_counted_anndata.h5ad"/> | |
91 <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/> | |
92 <param name="gmt_file" value="mouse_hallmark_ss.gmt"/> | |
93 <param name="gene_symbols_field" value="Symbol"/> | |
94 <param name="write_anndata" value="False"/> | |
95 <conditional name="gene_lists_source"> | |
96 <param name="source" value="gmt"/> | |
97 </conditional> | |
98 <output name="output_table"> | |
99 <assert_contents> | |
100 <has_n_columns n="3"/> | |
101 <has_text_matching expression="AUCell_HALLMARK_NOTCH_SIGNALING"/> | |
102 </assert_contents> | |
103 </output> | |
104 </test> | |
105 </tests> | |
106 <help> | |
107 **Description** | |
108 | |
109 This tool scores cells using the AUCell method for gene sets. | |
110 | |
111 **Input** | |
112 | |
113 The input file should be an AnnData object in H5AD format. The tool accepts an H5AD file containing raw or normalized data. | |
114 | |
115 The tool takes one of two input formats for specifying the gene sets to score: | |
116 | |
117 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. | |
118 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. | |
119 | |
120 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. | |
121 | |
122 You can also specify whether to use the raw data in the AnnData object instead of the X matrix using the "use_raw" parameter. | |
123 | |
124 **Output** | |
125 | |
126 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. | |
127 | |
128 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. | |
129 | |
130 **Example** | |
131 | |
132 | |
133 </help> | |
134 <citations> | |
135 <citation type="doi">10.1093/bioadv/vbac016</citation> | |
136 </citations> | |
137 </tool> |