comparison Marea/ras_generator.xml @ 48:e4235b5231e4 draft

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47:3af9d394367c

<tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.2">
    <description>- Reaction Activity Scores computation</description>
    <macros>
        <import>marea_macros.xml</import>
    </macros>
    <requirements>

            </when>
            <when value="Recon">
            </when>
            <when value="Custom">
                <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
                <conditional name="cond_map">
                    <param name="yes_no" type="select" label="Custom map? (optional)">
                        <option value="no" selected="true">no</option>
                        <option value="yes">yes</option>
                    </param>
                    <when value="yes">
                        <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
                    </when>
                    <when value="no">
                    </when>
                </conditional>
            </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" help="Default: Dataset" />
        <param name="none" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 

    <help>
<![CDATA[

What it does
-------------
]]>
    </help>
    <expand macro="citations" />
</tool>
	

48:e4235b5231e4

<tool id="MaREA RAS Generator" name="Expression2RAS" version="1.0.3">
    <description>- Reaction Activity Scores computation</description>
    <macros>
        <import>marea_macros.xml</import>
    </macros>
    <requirements>

            </when>
            <when value="Recon">
            </when>
            <when value="Custom">
                <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" 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" help="Default: Dataset" />
        <param name="none" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 

    <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>