<tool id="MaREA RAS Generator" name="Expression2RAS" version="2.0.0">
    <description>- Reaction Activity Scores computation</description>
    <macros>
        <import>marea_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.24.4">numpy</requirement>
        <requirement type="package" version="2.0.3">pandas</requirement>
        <requirement type="package" version="5.2.2">lxml</requirement>
		<requirement type="package" version="0.29.0">cobra</requirement>
	</requirements>
    <command detect_errors="exit_code">
        <![CDATA[
      	python $__tool_directory__/ras_generator.py
      	--rules_selector $cond_rule.rules_selector
        --input $input
        --none $none
        --tool_dir $__tool_directory__
        --out_log $log
        --ras_output $ras_output
        #if $cond_rule.rules_selector == 'Custom'
            --rule_list $rule_list
            --rules_name $rule_list.element_identifier
        #end if
        ]]>
    </command>
    <inputs>
        <conditional name="cond_rule">
            <expand macro="options"/>
            <when value="Custom">
                <param name="rule_list" argument="--rule_list" type="data" format="tabular, csv, pickle, p, pk" label="Custom rules" />
            </when>
        </conditional>
        <param name="input" argument="--input" type="data" format="tabular, csv, tsv" label="Gene Expression dataset:" />
        <param name="name" argument="--name" type="text" label="Dataset's name:" value="Dataset_RAS" help="Default: Dataset_RAS. Do not use white spaces." />
        <param name="none" argument="--none" type="boolean" checked="true" label="(A and NaN) solved as (A)?" /> 
    </inputs>

    <outputs>
        <data format="txt" name="log" label="Expression2RAS - $name - Log" />
        <data format="tabular" name="ras_output" label='$name'/>
    </outputs>

    <help>
<![CDATA[

What it does
-------------

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.
 
Accepted files:
    - A gene expression dataset
 
Format:
Tab-separated text file reporting the normalized expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column).
Column header: sample ID.
Row header: gene ID.
 
 
Optional files:
    - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:

	* (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
	* .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
 
Computation option ‘(A and NaN) solved as (A)’:
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’
 
If YES is selected: the GPR will be solved as A.
 
If NO is selected: the GPR will be disregarded tout-court (i.e., treated as NaN).

Example input
-------------

Custom GPR rules:

+------------+--------------------------------------+   
| id         |         rule (with entrez-id         |   
+============+======================================+   
| r1642      |             155060 or 10357          |   
+------------+--------------------------------------+    
| r1643      |        155060 or 100134869           |    
+------------+--------------------------------------+    
| r1640      |     155060 and 100134869 or 10357    |   
+------------+--------------------------------------+

RNA-seq dataset:

+------------+----------------+----------------+----------------+ 
| Hugo_ID    |   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
+============+================+================+================+
| HGNC:24086 |    0.523167    |    0.371355    |    0.925661    |  
+------------+----------------+----------------+----------------+    
| HGNC:24086 |    0.568765    |    0.765567    |    0.456789    |    
+------------+----------------+----------------+----------------+    
| HGNC:9876  |    0.876545    |    0.768933    |    0.987654    |  
+------------+----------------+----------------+----------------+
| HGNC:9     |    0.456788    |    0.876543    |    0.876542    |    
+------------+----------------+----------------+----------------+    
| HGNC:23    |    0.876543    |    0.786543    |    0.897654    |   
+------------+----------------+----------------+----------------+

]]>
    </help>
<expand macro="citations" />
</tool>