Mercurial > repos > ebi-gxa > score_genes_aucell

comparison decoupler_aucell_score.xml @ 1:e024d8280886 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 56273bcfbc0de8f6ab093f1131a7d22c05a70f25
author ebi-gxa
date Thu, 16 Nov 2023 20:05:21 +0000
parents 1e8697931d73
children e887a7e8c5b4
comparison
equal deleted inserted replaced
0:1e8697931d73 1:e024d8280886
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy0" profile="20.05"> 2 <tool id="score_genes_aucell" name="Decoupler AUCell" version="1.4.0+galaxy1" profile="20.05">
3 <description> 3 <description>
4 scores cells using the AUCell method for gene sets. 4 scores cells using the AUCell method for gene sets.
5 </description> 5 </description>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="1.4.0">decoupler</requirement> 7 <requirement type="package" version="1.4.0">decoupler</requirement>
8 </requirements> 8 </requirements>
9 <command> 9 <command>
10 python '$__tool_directory__/decoupler_aucell_score.py' 10 python '$__tool_directory__/decoupler_aucell_score.py'
11 --input_file '$input_file' 11 --input_file '$input_file'
12 #if $gene_lists_source.source == "gmt" 12 #if $gene_lists_source.source == "gmt"
13 --gmt_file '$gmt_file' 13 --gmt_file '$gene_lists_source.gmt_file'
14 --gene_sets_to_score '$gene_sets_to_score' 14 #if $gene_lists_source.gene_sets_to_score
15 --gene_sets_to_score '$gene_lists_source.gene_sets_to_score'
16 #end if
15 #else: 17 #else:
16 --gene_lists_to_score '$gene_lists_to_score' 18 --gene_lists_to_score '$gene_lists_source.gene_lists_to_score'
17 --score_names '$score_names' 19 --score_names '$gene_lists_source.score_names'
18 #end if 20 #end if
19 --gene_symbols_field '$gene_symbols_field' 21 --gene_symbols_field '$gene_symbols_field'
20 $use_raw 22 $use_raw
21 #if $write_anndata: 23 #if $write_anndata:
22 --write_anndata 24 --write_anndata
32 <option value="gmt" selected="true">Gene sets from GMT file</option> 34 <option value="gmt" selected="true">Gene sets from GMT file</option>
33 <option value="enumerated">Gene sets enumerated manually</option> 35 <option value="enumerated">Gene sets enumerated manually</option>
34 </param> 36 </param>
35 <when value="gmt"> 37 <when value="gmt">
36 <param name="gmt_file" type="data" format="txt" label="GMT file with gene sets" /> 38 <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" /> 39 <param name="gene_sets_to_score" type="text" optional="true" label="Gene sets to score within the GMT file" />
38 </when> 40 </when>
39 <when value="enumerated"> 41 <when value="enumerated">
40 <param name="gene_lists_to_score" type="text" label="Genes to score" /> 42 <param name="gene_lists_to_score" type="text" label="Genes to score" />
41 <param name="score_names" type="text" label="Score names" /> 43 <param name="score_names" type="text" label="Score names" />
42 </when> 44 </when>
54 </data> 56 </data>
55 </outputs> 57 </outputs>
56 <tests> 58 <tests>
57 <test expect_num_outputs="1"> 59 <test expect_num_outputs="1">
58 <param name="input_file" value="mito_counted_anndata.h5ad"/> 60 <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"/> 61 <param name="gene_symbols_field" value="Symbol"/>
62 <param name="write_anndata" value="true"/> 62 <param name="write_anndata" value="true"/>
63 <conditional name="gene_lists_source"> 63 <conditional name="gene_lists_source">
64 <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/>
65 <param name="gmt_file" value="mouse_hallmark_ss.gmt"/>
64 <param name="source" value="gmt"/> 66 <param name="source" value="gmt"/>
65 </conditional> 67 </conditional>
66 <output name="output_ad"> 68 <output name="output_ad">
67 <assert_contents> 69 <assert_contents>
68 <has_h5_keys keys="obs/AUCell_HALLMARK_NOTCH_SIGNALING"/> 70 <has_h5_keys keys="obs/AUCell_HALLMARK_NOTCH_SIGNALING"/>
70 </assert_contents> 72 </assert_contents>
71 </output> 73 </output>
72 </test> 74 </test>
73 <test expect_num_outputs="1"> 75 <test expect_num_outputs="1">
74 <param name="input_file" value="mito_counted_anndata.h5ad"/> 76 <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"/> 77 <param name="gene_symbols_field" value="Symbol"/>
76 <param name="score_names" value="TCell,Macro"/> 78 <param name="write_anndata" value="true"/>
79 <conditional name="gene_lists_source">
80 <param name="source" value="gmt"/>
81 <param name="gmt_file" value="mouse_hallmark_ss.gmt"/>
82 </conditional>
83 <output name="output_ad">
84 <assert_contents>
85 <has_h5_keys keys="obs/AUCell_HALLMARK_NOTCH_SIGNALING"/>
86 <has_h5_keys keys="obs/AUCell_HALLMARK_APICAL_SURFACE"/>
87 </assert_contents>
88 </output>
89 </test>
90 <test expect_num_outputs="1">
91 <param name="input_file" value="mito_counted_anndata.h5ad"/>
77 <param name="gene_symbols_field" value="Symbol"/> 92 <param name="gene_symbols_field" value="Symbol"/>
78 <param name="write_anndata" value="true"/> 93 <param name="write_anndata" value="true"/>
79 <conditional name="gene_lists_source"> 94 <conditional name="gene_lists_source">
80 <param name="source" value="enumerated"/> 95 <param name="source" value="enumerated"/>
96 <param name="gene_lists_to_score" value="Cd8b1,Cd8b2,Cd8a,Cd4,Nrp1,Cd80:Il1a,Il1b,Il6,Nos2,Tlr2,Tlr4,Cd80"/>
97 <param name="score_names" value="TCell,Macro"/>
81 </conditional> 98 </conditional>
82 <output name="output_ad"> 99 <output name="output_ad">
83 <assert_contents> 100 <assert_contents>
84 <has_h5_keys keys="obs/AUCell_TCell"/> 101 <has_h5_keys keys="obs/AUCell_TCell"/>
85 <has_h5_keys keys="obs/AUCell_Macro"/> 102 <has_h5_keys keys="obs/AUCell_Macro"/>
86 </assert_contents> 103 </assert_contents>
87 </output> 104 </output>
88 </test> 105 </test>
89 <test expect_num_outputs="1"> 106 <test expect_num_outputs="1">
90 <param name="input_file" value="mito_counted_anndata.h5ad"/> 107 <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"/> 108 <param name="gene_symbols_field" value="Symbol"/>
94 <param name="write_anndata" value="False"/> 109 <param name="write_anndata" value="False"/>
95 <conditional name="gene_lists_source"> 110 <conditional name="gene_lists_source">
96 <param name="source" value="gmt"/> 111 <param name="source" value="gmt"/>
112 <param name="gene_sets_to_score" value="HALLMARK_NOTCH_SIGNALING,HALLMARK_APICAL_SURFACE"/>
113 <param name="gmt_file" value="mouse_hallmark_ss.gmt"/>
97 </conditional> 114 </conditional>
98 <output name="output_table"> 115 <output name="output_table">
99 <assert_contents> 116 <assert_contents>
100 <has_n_columns n="3"/> 117 <has_n_columns n="3"/>
101 <has_text_matching expression="AUCell_HALLMARK_NOTCH_SIGNALING"/> 118 <has_text_matching expression="AUCell_HALLMARK_NOTCH_SIGNALING"/>