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1 <tool id="MaREA RAS Generator" name="Expression2RAS" version="2.0.0">
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2 <description>- Reaction Activity Scores computation</description>
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3 <macros>
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4 <import>marea_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="1.24.4">numpy</requirement>
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8 <requirement type="package" version="2.0.3">pandas</requirement>
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9 <requirement type="package" version="5.2.2">lxml</requirement>
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10 <requirement type="package" version="0.29.0">cobra</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code">
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13 <![CDATA[
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14 python $__tool_directory__/ras_generator.py
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15 --rules_selector $cond_rule.rules_selector
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16 --input $input
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17 --none $none
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18 --tool_dir $__tool_directory__
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19 --out_log $log
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20 --ras_output $ras_output
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21 #if $cond_rule.rules_selector == 'Custom'
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22 --rule_list $rule_list
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23 --rules_name $rule_list.element_identifier
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24 #end if
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25 ]]>
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26 </command>
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27 <inputs>
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28 <conditional name="cond_rule">
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29 <expand macro="options"/>
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30 <when value="Custom">
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31 <param name="rule_list" argument="--rule_list" type="data" format="tabular, csv, pickle, p, pk" label="Custom rules" />
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32 </when>
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33 </conditional>
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34 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
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35 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
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36 <param name="none" argument="--none" type="boolean" checked="true" label="(A and NaN) solved as (A)?" />
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37 </inputs>
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38
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39 <outputs>
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40 <data format="txt" name="log" label="Expression2RAS - $name - Log" />
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41 <data format="tabular" name="ras_output" label="$name RAS"/>
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42 </outputs>
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43
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44 <help>
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45 <![CDATA[
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46
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47 What it does
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48 -------------
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49
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50 This tool computes Reaction Activity Scores from gene expression (RNA-seq) dataset(s), as described in Graudenzi et al. Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. Journal of Biomedical Informatics, 2018, 87: 37-49.
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51
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52 Accepted files:
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53 - A gene expression dataset
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54
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55 Format:
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56 Tab-separated text file reporting the normalized expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column).
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57 Column header: sample ID.
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58 Row header: gene ID.
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59
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60
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61 Optional files:
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62 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
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63
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64 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
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65 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
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66
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67 Computation option ‘(A and NaN) solved as (A)’:
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68 In case of missing expression value, referred to as NaN (Not a Number), for a gene joined with an AND operator in a given GPR rule, the rule ‘A and NaN’
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69
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70 If YES is selected: the GPR will be solved as A.
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71
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72 If NO is selected: the GPR will be disregarded tout-court (i.e., treated as NaN).
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73
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74 Example input
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75 -------------
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76
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77 Custom GPR rules:
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78
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79 +------------+--------------------------------------+
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80 | id | rule (with entrez-id |
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81 +============+======================================+
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82 | r1642 | 155060 or 10357 |
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83 +------------+--------------------------------------+
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84 | r1643 | 155060 or 100134869 |
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85 +------------+--------------------------------------+
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86 | r1640 | 155060 and 100134869 or 10357 |
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87 +------------+--------------------------------------+
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88
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89 RNA-seq dataset:
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90
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91 +------------+----------------+----------------+----------------+
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92 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
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93 +============+================+================+================+
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94 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
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95 +------------+----------------+----------------+----------------+
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96 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
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97 +------------+----------------+----------------+----------------+
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98 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
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99 +------------+----------------+----------------+----------------+
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100 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
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101 +------------+----------------+----------------+----------------+
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102 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
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103 +------------+----------------+----------------+----------------+
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104
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105 ]]>
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106 </help>
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107 <expand macro="citations" />
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108 </tool>
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109
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