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annotate decoupler_pathway_inference.xml @ 2:82b7cd3e1bbd draft

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author ebi-gxa
date Tue, 16 Apr 2024 11:49:19 +0000
parents 77d680b36e23
children 9864fd2cc1f0
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1 <tool id="decoupler_pathway_inference" name="Decoupler Pathway Inference" version="1.4.0+galaxy0" profile="20.05" license="MIT">
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2 <description>
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3 of functional genesets/pathways for scRNA-seq data.
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.4.0">decoupler</requirement>
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7 </requirements>
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8 <command>
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9 python '$__tool_directory__/decoupler_pathway_inference.py'
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10 -i '$input_anndata'
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11 -n '$input_network_file'
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12 --min_n "$min_n"
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13 --method '$method'
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14 $use_raw
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15 --source $source
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16 --target $target
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17 --weight $weight
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18 --output "inference"
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19 $write_activities_path
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20 </command>
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21 <inputs>
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22 <param name="input_anndata" type="data" format="h5ad" label="Input AnnData file" />
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23 <param name="input_network_file" type="data" format="tabular" label="Input Network file" help="Tabular file with columns Source, Target and Weight. A source gene/pathway regulates/contains a target gene, weights can be either positive or negative. The source element needs to be part of the network, the target is a gene in the network and in the dataset" />
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24 <param name="min_n" type="integer" min="0" value="5" label="Minimum targets per source." help="If targets are less than minimum, sources are removed" />
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25 <param name="method" type="select" label="Activity inference method">
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26 <option value="mlm" selected="true">Multivariate linear model (MLM)</option>
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27 <option value="ulm">Univariate linear model (ULM)</option>
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28 </param>
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29 <param name="use_raw" type="boolean" truevalue="--use_raw" falsevalue="" checked="false" label="Use the raw part of the AnnData object" />
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30 <param name="write_activities_path" type="boolean" truevalue="--activities_path anndata_activities_path.h5ad" falsevalue="" checked="true" label="Write the activities AnnData object (contains the MLM/ULM activity results for each pathway and each cell in the main matrix, it is not a replacement of the original AnnData provided as input)." />
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31 <param name="source" type="text" value='source' label="Column name in network with source nodes." help="If empty then default is 'source' is used." />
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32 <param name="target" type="text" value='target' label="Column name in network with target nodes." help="If empty then default is 'target' is used." />
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33 <param name="weight" type="text" value='weight' label="Column name in network with weight." help="If empty then default is 'weight' is used." />
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34 </inputs>
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35 <outputs>
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36 <data name="output_ad" format="h5ad" from_work_dir="anndata_activities_path.h5ad" label="${tool.name} on ${on_string}: Regulators/Pathways activity AnnData file">
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37 <filter>write_activities_path</filter>
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38 </data>
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39 <data name="output_table" format="tabular" from_work_dir="inference.tsv" label="${tool.name} on ${on_string}: Output estimate table" />
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40 </outputs>
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41 <tests>
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42 <!-- Hint: You can use [ctrl+alt+t] after defining the inputs/outputs to auto-scaffold some basic test cases. -->
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43
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44 <test expect_num_outputs="2">
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45 <param name="input_anndata" value="pbmc3k_processed.h5ad"/>
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46 <param name="input_network_file" value="progeny_test.tsv"/>
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47 <param name="min_n" value="0"/>
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48 <param name="method" value="mlm"/>
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49 <param name="use_raw" value="false"/>
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50 <param name="write_activities_path" value="true"/>
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51 <param name="source" value="source"/>
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52 <param name="target" value="target"/>
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53 <param name="weight" value="weight"/>
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54 <output name="output_ad">
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55 <assert_contents>
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56 <has_h5_keys keys="obsm/mlm_estimate"/>
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57 </assert_contents>
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58 </output>
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59 <output name="output_table">
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60 <assert_contents>
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61 <has_n_columns n="5"/>
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62 </assert_contents>
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63 </output>
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64 </test>
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65 <test>
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66 <param name="input_anndata" value="pbmc3k_processed.h5ad"/>
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67 <param name="input_network_file" value="progeny_test_2.tsv"/>
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68 <param name="min_n" value="0"/>
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69 <param name="method" value="ulm"/>
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70 <param name="use_raw" value="false"/>
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71 <param name="write_activities_path" value="true"/>
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72 <param name="source" value="source"/>
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73 <param name="target" value="target"/>
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74 <param name="weight" value="weight"/>
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75 <output name="output_ad">
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76 <assert_contents>
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77 <has_h5_keys keys="obsm/ulm_estimate"/>
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78 </assert_contents>
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79 </output>
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80 <output name="output_table">
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81 <assert_contents>
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82 <has_n_columns n="5"/>
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83 </assert_contents>
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84 </output>
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85 </test>
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86 </tests>
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87 <help>
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88 **What it does**
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89
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90 Usage
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91 .....
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92
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93
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94 **Description**
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95
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96 This tool extracts pathway activity inference using decoupler.
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97
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98 **Input**
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99
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100 The input file should be an AnnData object in H5AD format. The tool accepts an H5AD file containing raw or normalized data.
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101
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102 The tool also takes network file containing a collection of pathways and their target genes, with weights for each interaction.
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103 Example:
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104 ```
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105 source target weight
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106 0 T1 G01 1.0
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107 1 T1 G02 1.0
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108 2 T1 G03 0.7
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109 3 T2 G04 1.0
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110 4 T2 G06 -0.5
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111 ```
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112
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113 You can also specify whether to use the raw data in the AnnData object instead of the X matrix using the "use_raw" parameter and Minimum of targets per source using "min_n".
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114
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115
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116 **Output**
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117
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118 The tool outputs an AnnData object containing the scores in the "obs" field, and tab-separated text files containing the scores for each cell.
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119
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120 If the "write_activities_path" parameter is set to "true", the tool will write the modified AnnData object to an H5AD file.
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121 If the "write_inference" parameter is set to "true", the tool will output a tab-separated text file containing the scores for each cell.
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122
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123
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124
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125 </help>
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126 <citations>
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127 <citation type="doi">10.1093/bioadv/vbac016 </citation>
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128 </citations>
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129 </tool>