Mercurial > repos > iuc > gem_knockout

annotate gem_knockout.xml @ 0:1cea77c3c471 draft default tip

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planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
author iuc
date Fri, 13 Dec 2024 21:33:47 +0000
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0
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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1 <tool id="gem_knockout" name="Gene knockout analysis" version="@VERSION@" profile="@PROFILE@">
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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2 <description>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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3 on a GEM
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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4 </description>
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iuc
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5 <macros>
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iuc
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6 <import>gem_macros.xml</import>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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7 </macros>
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iuc
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8 <expand macro="requirements"/>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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9 <expand macro="version_command_cobra"/>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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10 <command>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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11 python '$__tool_directory__/gem_knockout.py'
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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12 --cb_model_location '${cb_model_location}'
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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13 --output '${output}'
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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14 --knockout_type '${knockout_type}'
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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15 #if $gene_knockouts:
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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16 --gene_knockouts '${gene_knockouts}'
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17 #end if
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18 #if $uptake_constraints_file:
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19 --uptake_constraints_file '${uptake_constraints_file}'
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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20 #end if
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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21 </command>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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22 <inputs>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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23 <expand macro="input_model"/>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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24 <param name="knockout_type" type="select" label="Type of knockout analysis">
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25 <option value="single">Single gene knockouts</option>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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26 <option value="double">Double gene knockouts</option>
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27 </param>
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28 <param name="gene_knockouts" type="text" optional="true" label="Specific genes to knockout (comma-separated)" help="Leave empty to analyze all genes">
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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29 <validator type="regex" message="Genes must be comma-separated, alphanumeric, and underscore characters only">^([a-zA-Z0-9_]+,?)+$</validator>
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30 </param>
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31 <expand macro="input_uptake_constraints"/>
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32 </inputs>
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33 <outputs>
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34 <expand macro="output"/>
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35 </outputs>
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36 <tests>
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37 <!-- Test 1: Single gene knockout analysis -->
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38 <test>
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39 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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40 <param name="knockout_type" value="single"/>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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41 <output name="output" file="expected_single_knockout.csv"/>
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42 </test>
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43 <!-- Test 2: Single gene knockout analysis with specific genes -->
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44 <test>
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45 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
1cea77c3c471 planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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46 <param name="knockout_type" value="single"/>
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47 <param name="gene_knockouts" value="b0351,b2296"/>
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48 <output name="output">
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49 <assert_contents>
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50 <has_line line="reaction_id;ko_gene_id_1;ko_gene_id_2;reaction;wildtype_flux;knockout_flux"/>
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51 </assert_contents>
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52 </output>
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53 </test>
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54 <!-- Test 3: Double gene knockout analysis -->
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55 <test>
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56 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
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57 <param name="knockout_type" value="double"/>
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58 <param name="gene_knockouts" value="b0351,b2296,b1849"/>
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59 <output name="output">
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60 <assert_contents>
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61 <has_line line="reaction_id;ko_gene_id_1;ko_gene_id_2;reaction;wildtype_flux;knockout_flux"/>
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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 4: Single gene knockout analysis with uptake constraints -->
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66 <test>
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67 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
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68 <param name="knockout_type" value="single"/>
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69 <param name="uptake_constraints_file" value="textbook_model_cobrapy_exchange.csv"/>
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70 <output name="output">
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71 <assert_contents>
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72 <has_line line="reaction_id;ko_gene_id_1;ko_gene_id_2;reaction;wildtype_flux;knockout_flux"/>
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73 </assert_contents>
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74 </output>
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75 </test>
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76 <!-- Test 5: Double gene knockout analysis with invalid model file -->
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77 <test expect_failure="true">
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78 <param name="cb_model_location" value="invalid_format.txt"/>
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79 <assert_stderr>
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80 <has_text text="The model could not be read"/>
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81 </assert_stderr>
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82 </test>
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83 <!-- Test 5: Double gene knockout analysis with invalid gene names -->
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84 <test expect_failure="true">
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85 <param name="cb_model_location" value="textbook_model_cobrapy.xml"/>
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86 <param name="knockout_type" value="double"/>
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87 <param name="gene_knockouts" value="abc,123"/>
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88 <assert_stderr>
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89 <has_text text="One or more of the genes to knockout are not present in the model"/>
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90 </assert_stderr>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 Gene Knockout Analysis
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95
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96 This tool performs single or double gene knockout analysis on a Genome-scale Metabolic Model (GEM) using Flux Balance Analysis (FBA).
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97
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98 Input Parameters
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99
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100 **Model File**: A GEM in SBML format (.xml) that will be analyzed.
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101
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102 **Knockout Type**: Choose between:
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103 - Single gene knockouts: Analyze the effect of removing one gene at a time
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104 - Double gene knockouts: Analyze the effect of removing pairs of genes
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105
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106 **Genes to Knockout** (optional): Specify particular genes to analyze. If left empty, all genes in the model will be analyzed.
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107
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108 **Uptake Constraints File** (optional): A CSV file specifying constraints for exchange reactions.
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109
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110 Output
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111
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112 The tool generates a CSV file containing:
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113 - Reaction IDs
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114 - Knocked out gene(s)
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115 - Reaction formulas
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116 - Wildtype flux values
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117 - Knockout flux values
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118
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119 Common Issues
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120
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121 - Ensure your model is well-formatted
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122 - Verify that specified genes exist in the model
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123 - Large models may require significant computation time, especially for double knockouts
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124 ]]></help>
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125 <citations>
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126 <expand macro="citation_cobrapy"/>
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127 </citations>
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128 </tool>