4
+ − 1 <tool id="MaREA RAS Generator" name="Expression2RAS" version="2.0.0">
+ − 2 <description>- Reaction Activity Scores computation</description>
+ − 3 <macros>
+ − 4 <import>marea_macros.xml</import>
+ − 5 </macros>
+ − 6 <requirements>
+ − 7 <requirement type="package" version="1.24.4">numpy</requirement>
+ − 8 <requirement type="package" version="2.0.3">pandas</requirement>
+ − 9 <requirement type="package" version="5.2.2">lxml</requirement>
+ − 10 <requirement type="package" version="0.29.0">cobra</requirement>
+ − 11 </requirements>
+ − 12 <command detect_errors="exit_code">
+ − 13 <![CDATA[
+ − 14 python $__tool_directory__/ras_generator.py
+ − 15 --rules_selector $cond_rule.rules_selector
+ − 16 --input $input
+ − 17 --none $none
+ − 18 --tool_dir $__tool_directory__
+ − 19 --out_log $log
+ − 20 --ras_output $ras_output
+ − 21 #if $cond_rule.rules_selector == 'Custom'
+ − 22 --rule_list $rule_list
+ − 23 --rules_name $rule_list.element_identifier
+ − 24 #end if
+ − 25 ]]>
+ − 26 </command>
+ − 27 <inputs>
+ − 28 <conditional name="cond_rule">
+ − 29 <expand macro="options"/>
+ − 30 <when value="Custom">
+ − 31 <param name="rule_list" argument="--rule_list" type="data" format="tabular, csv, pickle, p, pk" label="Custom rules" />
+ − 32 </when>
+ − 33 </conditional>
+ − 34 <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
+ − 35 <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
+ − 36 <param name="none" argument="--none" type="boolean" checked="true" label="(A and NaN) solved as (A)?" />
+ − 37 </inputs>
+ − 38
+ − 39 <outputs>
+ − 40 <data format="txt" name="log" label="Expression2RAS - $name - Log" />
65
+ − 41 <!--<data format="tabular" name="ras_output" label="$name RAS"/>-->
+ − 42 <data format="tabular" name="ras_output" label="$name"/> <!--To be ready for RAS to bounds in case of multiple RAs matrices (class name extracted from file name)-->
4
+ − 43 </outputs>
+ − 44
+ − 45 <help>
+ − 46 <![CDATA[
+ − 47
+ − 48 What it does
+ − 49 -------------
+ − 50
+ − 51 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.
+ − 52
+ − 53 Accepted files:
+ − 54 - A gene expression dataset
+ − 55
+ − 56 Format:
+ − 57 Tab-separated text file reporting the normalized expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column).
+ − 58 Column header: sample ID.
+ − 59 Row header: gene ID.
+ − 60
+ − 61
+ − 62 Optional files:
+ − 63 - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
+ − 64
+ − 65 * (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
+ − 66 * .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
+ − 67
+ − 68 Computation option ‘(A and NaN) solved as (A)’:
+ − 69 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’
+ − 70
+ − 71 If YES is selected: the GPR will be solved as A.
+ − 72
+ − 73 If NO is selected: the GPR will be disregarded tout-court (i.e., treated as NaN).
+ − 74
+ − 75 Example input
+ − 76 -------------
+ − 77
+ − 78 Custom GPR rules:
+ − 79
+ − 80 +------------+--------------------------------------+
+ − 81 | id | rule (with entrez-id |
+ − 82 +============+======================================+
+ − 83 | r1642 | 155060 or 10357 |
+ − 84 +------------+--------------------------------------+
+ − 85 | r1643 | 155060 or 100134869 |
+ − 86 +------------+--------------------------------------+
+ − 87 | r1640 | 155060 and 100134869 or 10357 |
+ − 88 +------------+--------------------------------------+
+ − 89
+ − 90 RNA-seq dataset:
+ − 91
+ − 92 +------------+----------------+----------------+----------------+
+ − 93 | Hugo_ID | TCGAA62670 | TCGAA62671 | TCGAA62672 |
+ − 94 +============+================+================+================+
+ − 95 | HGNC:24086 | 0.523167 | 0.371355 | 0.925661 |
+ − 96 +------------+----------------+----------------+----------------+
+ − 97 | HGNC:24086 | 0.568765 | 0.765567 | 0.456789 |
+ − 98 +------------+----------------+----------------+----------------+
+ − 99 | HGNC:9876 | 0.876545 | 0.768933 | 0.987654 |
+ − 100 +------------+----------------+----------------+----------------+
+ − 101 | HGNC:9 | 0.456788 | 0.876543 | 0.876542 |
+ − 102 +------------+----------------+----------------+----------------+
+ − 103 | HGNC:23 | 0.876543 | 0.786543 | 0.897654 |
+ − 104 +------------+----------------+----------------+----------------+
+ − 105
+ − 106 ]]>
+ − 107 </help>
+ − 108 <expand macro="citations" />
+ − 109 </tool>
+ − 110