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changeset 1:9e63d5f02d62 draft

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Uploaded
author bimib
date Wed, 07 Nov 2018 07:07:46 -0500
parents 23ac9cf12788
children 3b3d0e5d0802
files Marea/marea.xml Marea/marea_cluster.xml Marea/marea_macros.xml
diffstat 3 files changed, 242 insertions(+), 148 deletions(-) [+]
line wrap: on
line diff
--- a/Marea/marea.xml	Tue Nov 06 03:16:21 2018 -0500
+++ b/Marea/marea.xml	Wed Nov 07 07:07:46 2018 -0500
@@ -1,15 +1,15 @@
 <tool id="MaREA" name="Metabolic Enrichment Analysis">
     <description>for Galaxy</description>
+    <macros>
+        <import>marea_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <requirements>
-        <requirement type="package">pandas</requirement>
-        <requirement type="package">scipy</requirement>
         <requirement type="package">lxml</requirement>
         <requirement type="package">svglib</requirement>
         <requirement type="package">reportlab</requirement>
-        <requirement type="package">cobrapy</requirement>
-        <requirement type="package">python-libsbml</requirement>
     </requirements>
-    <command>
+    <command detect_errors="exit_code">
         <![CDATA[
       	python $__tool_directory__/marea.py
         --rules_selector $cond_rule.rules_selector
@@ -41,60 +41,67 @@
         #end if
         ]]>
     </command>
+
     <inputs>
         <conditional name="cond_rule">
-            <param name="rules_selector" type="select" label="Gene-Protein-Reaction rules:">
-                <option value="HMRcore" selected="true">HMRcore rules</option>
-                <option value="Recon">Recon 2.2 rules</option>
-                <option value="Custom">Custom rules</option>
-            </param>
+            <expand macro="options" />
+            <when value="HMRcore">
+            </when>
+            <when value="Recon">
+            </when>
             <when value="Custom">
-                <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules"/>
+                <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" type="data" format="xml, svg" label="custom-map.svg"/>
+                        <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
+                    </when>
+                    <when value="no">
                     </when>
                 </conditional>
             </when>
         </conditional>
         <conditional name="cond">
-            <param name="type_selector" type="select" label="Input format:">
-                <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + … + RNAseq of group N</option>
+            <param name="type_selector" argument="--option" type="select" label="Input format:">
+                <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option>
                 <option value="dataset_class">RNAseq of all samples + sample group specification</option>
             </param>
             <when value="datasets">
                 <repeat name="input_Datasets" title="RNAseq" type="data" min="2">
-                    <param name="input" type="data" format="tabular, csv, tsv" label="add dataset"/>	
-                    <param name="input_name" type="text" label="Dataset's name:" value="Dataset" help="Defalut: Dataset"/>
+                    <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" />	
+                    <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Defalut: Dataset" />
 	        </repeat>
             </when>
             <when value="dataset_class">
-                <param name="input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples"/>
-                <param name="input_class" type="data" format="tabular, csv, tsv" label="Sample group specification"/>
+                <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
+                <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" />
             </when>
         </conditional>
-        <param name="None" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?"/> 
-        <param name="pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold" help="min value 0"/>
-        <param name="fChange" type="float" size="20" value="1.5" min="1" label="Fold-Cahnge threshold" help="min value 1"/>
+        <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> 
+        <param name="pValue" argument="--pValue" type="float" size="20" value="0.05" max="1" min="0" label="P-value threshold" help="min value 0" />
+        <param name="fChange" argument="--fChange" type="float" size="20" value="1.5" min="1" label="Fold-Change threshold" help="min value 1" />
     </inputs>
+
     <outputs>
-        <data format="txt" name="log" label="Log"/>
-        <collection name="map_svg" type="list" label="file svg">
+        <data format="txt" name="log" label="Log" />
+        <collection name="map_svg" type="list" label="Graphical results (.svg)">
             <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter>
-            <discover_datasets pattern="__name_and_ext__" directory="map_svg"/>
+            <discover_datasets pattern="__name_and_ext__" directory="map_svg" />
         </collection>
-        <collection name="map_pdf" type="list" label="file pdf">
+        <collection name="map_pdf" type="list" label="Graphical results (.pdf)">
             <filter>(cond_rule['rules_selector'] == 'HMRcore') or ((cond_rule['rules_selector'] == 'Custom') and (cond_rule['cond_map']['yes_no'] == 'yes'))</filter>
-            <discover_datasets pattern="__name_and_ext__" directory="map_pdf"/>
+            <discover_datasets pattern="__name_and_ext__" directory="map_pdf" />
         </collection>
-        <collection name="table_out" type="list" label="file table">
-            <discover_datasets pattern="__name_and_ext__" directory="table_out"/>
+        <collection name="table_out" type="list" label="Tabular results">
+            <discover_datasets pattern="__name_and_ext__" directory="table_out" />
         </collection>
     </outputs>
+
+    
+
     <help>
 <![CDATA[
 
@@ -103,87 +110,55 @@
 
 This tool analyzes RNA-seq dataset(s) as described in Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724.
 
-The tool can be used to generate:
-    1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes
-    2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes
-    3) a log file (.txt) 
+Accepted files are: 
+    - option 1) two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. "*classA*" and "*classB*");
+    - option 2) one RNA dataset and one class-file specifying the class/condition each sample belongs to.
+
+Optional files:
+    - custom GPR (Gene-Protein-Reaction) rules. Two accepted formats:
 
-Accepted files are: 
-    1) or two or more RNA-seq datasets, each referring to samples in a given condition/class. The user can specify a label for each class (as e.g. “classA” and “classB”).
-    2) or one RNA dataset and one class-file specifying the class/condition each sample belongs to.
+	* (Cobra Toolbox and CobraPy compliant) xml of metabolic model;
+	* .csv file specifyig for each reaction ID (column 1) the corresponding GPR rule (column 2).
+    - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
 
+The tool generates:
+    1) a tab-separated file: reporting fold-change and p-values of reaction activity scores (RASs) between a pair of conditions/classes;
+    2) a metabolic map file (downlodable as .svg): visualizing up- and down-regulated reactions between a pair of conditions/classes;
+    3) a log file (.txt).
 
-RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, …) of each gene (row) for a given sample (column). Header: sample ID.
+RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID.
 
 Class-file format: each row of the class-file reports the sample ID (column1) and the label of the class/condition the sample belongs to (column 2).
 
 To calculate P-Values and Fold-Changes and to generate maps, comparisons are performed for each possible pair of classes.
 
-Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label “classA”.
-
-.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
+Output files will be named as classA_vs_classB. Reactions will conventionally be reported as up-regulated (down-regulated) if they are significantly more (less) active in class having label "classA".
 
 
 Example input
 -------------
 
-**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N" exemple input"** option:
+**"Custom Rules"** option:
+
+Custom Rules Dastaset:
 
-Dataset 1:						
+@CUSTOM_RULES_EXEMPLE@
+
+**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
 
-+------------+------------+------------+------------+   
-|  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  |   
-+------------+------------+------------+------------+ 
-   
-|
+RNA-seq Dataset 1:						
+
+@DATASET_EXEMPLE1@
 
-Dataset 2:
+RNA-seq Dataset 2:
 
-+-------------+------------+------------+------------+
-| Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
-+=============+============+============+============+
-|    A1BG     |  0.523167  |  0.371355  |  0.925661  |
-+-------------+------------+------------+------------+
-|    A1CF     |  0.568765  |  0.765567  |  0.456789  |
-+-------------+------------+------------+------------+
-|     A2M     |  0.876545  |  0.768933  |  0.987654  |
-+-------------+------------+------------+------------+
-|    A4GALT   |  0.456788  |  0.876543  |  0.876542  |
-+-------------+------------+------------+------------+
-|   M664Y65   |  0.876543  |  0.786543  |  0.897654  |
-+-------------+------------+------------+------------+
-
-|
+@DATASET_EXEMPLE2@
 
 **"RNAseq of all samples + sample group specification"** option:
 
-Dataset:
+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  |   
-+------------+------------+------------+------------+ 
-
-|
+@DATASET_EXEMPLE1@
 
 Class-file:
 
@@ -199,42 +174,22 @@
 
 |
 
-
-
-.. class:: warningmark
-
-This tool expects input datasets consisting of tab-delimited columns.
-
-
 .. class:: infomark
 
-TIP: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
+**TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
 
 .. class:: infomark
 
-TIP: If your dataset is not split into classes, use `Cluster for MaREA`_.
+**TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_.
 
-This tool is developed by the `nome del gruppo di bioinformatica`_ at the `dipartimento di informatica disco`_.
-
+@REFERENCE@
 
+.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
 .. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
-.. _Cluster for MaREA: http://link del tool di cluster.org/
-.. _nome del gruppo di bioinformatica: http://sito di bio.org
-.. _dipartimento di informatica disco : http://www.disco.unimib.it/go/Home/English
+.. _MaREA cluster analysis: http://link del tool di cluster.org
 
 ]]>
     </help>
+    <expand macro="citations" />
 </tool>
 	
-	
-	
-	
-	
-	
-	
-	
-	
-	
-	
-	
-	
--- a/Marea/marea_cluster.xml	Tue Nov 06 03:16:21 2018 -0500
+++ b/Marea/marea_cluster.xml	Wed Nov 07 07:07:46 2018 -0500
@@ -1,12 +1,12 @@
 <tool id="MaREA_cluester" name="MaREA cluster analysis">
     <description>of Reaction Activity Scores</description>
+    <macros>
+        <import>marea_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <requirements>
-        <requirement type="package">pandas</requirement>
         <requirement type="package">scikit-learn</requirement>
-        <requirement type="package">scipy</requirement>
         <requirement type="package">matplotlib</requirement>
-        <requirement type="package">cobrapy</requirement>
-        <requirement type="package">python-libsbml</requirement>
     </requirements>
     <command>
         <![CDATA[
@@ -32,27 +32,23 @@
     </command>
     <inputs>
         <conditional name="cond_rule">
-            <param name="rules_selector" type="select" label="Gene-Protein-Reaction rules:">
-                <option value="HMRcore" selected="true">HMRcore rules</option>
-                <option value="Recon">Recon 2.2 rules</option>
-                <option value="Custom">Custom rules</option>
-            </param>
+            <expand macro="options" />
             <when value="Custom">
-                <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules"/>
+                <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" />
             </when>
         </conditional>
-        <param name="input" type="data" format="tabular, csv, tsv" label="RNAseq of all samples"/>
-        <param name="name" type="text" label="Output name prefix" value = "dataset"/>
-        <param name="k_min" type="integer" size="20" value="3" min="2" max="30" label="min number of clusters (k) to be tested (k-means)"/>
-        <param name="k_max" type="integer" size="20" value="3" min="2" max="30" label="max number of clusters (k) to be tested (k-means)"/>
-        <param name="None" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" help="if NO is selected (A and NaN) is solved as (NaN)"/>
+        <param name="input" argument="--data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" />
+        <param name="name" argument="--name" type="text" label="Output name prefix" value="dataset" />
+        <param name="k_min" argument="--k_min" type="integer" size="20" value="3" min="2" max="30" label="Min number of clusters (k) to be tested (k-means)"/>
+        <param name="k_max" argument="--k_max" type="integer" size="20" value="3" min="2" max="30" label="Max number of clusters (k) to be tested (k-means)"/>
+        <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" help="If NO is selected, (A and NaN) is solved as (NaN)" />
 	<conditional name="cond_hier">
-            <param name="hier" type="select" label="Produce dendrogram (hierarchical clustering):">
+            <param name="hier" argument="--cond_hier" type="select" label="Produce dendrogram (hierarchical clustering):">
                 <option value="no" selected="true">no</option>
                 <option value="yes">yes</option>
             </param>
             <when value="yes">
-                <param name="linkage" type="select" label="Linkage type:">
+                <param name="linkage" argument="--linkage" type="select" label="Linkage type:">
                     <option value="single" selected="true">Single: minimum distance between all observations of two sets</option>
                     <option value="complete">Complete: maximum distance between all observations of two sets</option>
                     <option value="average">Average: average distance between all observations of two sets</option>
@@ -60,38 +56,80 @@
             </when>
         </conditional>
     </inputs>
+
     <outputs>
-        <data format="txt" name="log" label="Log"/>
+        <data format="txt" name="log" label="Log" />
         <data format="pdf" name="dendrogram" label="$name dendrogram">
             <filter>cond_hier['hier'] == 'yes'</filter>
         </data>
-        <data format="pdf" name="elbow" label="$name elbow evaluation method"/>
+        <data format="pdf" name="elbow" label="$name elbow evaluation method" />
         <collection name="cluster_out" type="list" label="Clusters $k_min - $k_max">
-            <discover_datasets pattern="__name_and_ext__" directory="cluster_out"/>
+            <discover_datasets pattern="__name_and_ext__" directory="cluster_out" />
         </collection>
     </outputs>
+
     <help>
+<![CDATA[
+
+What it does
+-------------
+
+This tool performs cluster analysis of RNA-seq dataset(s) based of Graudenzi et al."`MaREA`_: Metabolic feature extraction, enrichment and visualization of RNAseq data" bioRxiv (2018): 248724.
+
+Accepted files are:
+    1) For "Recon 2.2 rules" or "HMRcore rules" options: RNA-seq dataset. The user can specify a label of output prefix (as e.g. "K=3 *dataset*" and "K=4 *MyDataset*");
+    2) For "Custom rules" option: custom rules dataset, custom map (.svg) and RNA-seq dataset. The user can specify a label of output prefix (as e.g. "K=3 *dataset*" and "K=4 *MyDataset*").
+
+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).
+    - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
 
-.. class:: warningmark
+The tool generates:
+    1) Clusters n1 - n2 (n1 and n2 refer to min and max number of clusters): class-files (as many files as the chosen different number of clusters k to be tested) specifying the class/condition each sample belongs to;
+    2) Log: a log file (.txt);
+    3) *dataset* elbow evaluation method: diagram (.pdf) of elbow evaluation method;
+    4) *dataset* dendrogram (optional): dendrogram (.pdf) if the user chooses to produce a dendrogram (hierachical clustering).
+
+RNA-seq datasets format: tab-separated text files, reporting the expression level (e.g., TPM, RPKM, ...) of each gene (row) for a given sample (column). Header: sample ID.
+
+
+Example input
+-------------
 
-This tool expects input datasets consisting of tab-delimited columns.
+**RNA-seq dataset**:						
+
+@DATASET_EXEMPLE@
+
+**Custom Rules Dataset**:
+
+@CUSTOM_RULES_EXEMPLE@
+
+**Custom Map**:
+
+*see the generated HMRcore .svg map for example*
+
+
 
 .. class:: infomark
 
-**TIP:** If your data is not TAB delimited, use *Text Manipulation > Convert delimiters to TAB*
+**TIP**: If your data is not TAB delimited, use `Convert delimiters to TAB`_.
+
+.. class:: warningmark
+
+If dendrogram it's too populated, each path and label can be not clear.
+
+@REFERENCE@
 
+.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724
+.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj
+
+
+]]>
     </help>
+    <expand macro="citations" />
 </tool>
 	
 	
-	
-	
-	
-	
-	
-	
-	
-	
-	
-	
-	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Marea/marea_macros.xml	Wed Nov 07 07:07:46 2018 -0500
@@ -0,0 +1,101 @@
+<macros>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package">pandas</requirement>
+            <requirement type="package">scipy</requirement>
+            <requirement type="package">cobrapy</requirement>
+            <requirement type="package">python-libsbml</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="options">
+        <param name="rules_selector" argument="--rules_selector" type="select" label="Gene-Protein-Reaction rules:">
+            <option value="HMRcore" selected="true">HMRcore rules</option>
+            <option value="Recon">Recon 2.2 rules</option>
+            <option value="Custom">Custom rules</option>
+        </param>
+    </xml>
+
+   <token name="@CUSTOM_RULES_EXEMPLE@">
+
++--------------------+-------------------------------+
+|         id         |     rule (with entrez-id)     |
++====================+===============================+
+|        SHMT1       |        155060 or 10357        |
++--------------------+-------------------------------+
+|        NIT2        |      155060 or 100134869      |
++--------------------+-------------------------------+
+| GOT1_GOT2_GOT1L1_2 | 155060 and 100134869 or 10357 |
++--------------------+-------------------------------+
+
+|
+
+    </token>
+
+    <token name="@DATASET_EXEMPLE1@">
+
++------------+------------+------------+------------+   
+|  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  |   
++------------+------------+------------+------------+ 
+   
+|
+
+    </token>
+
+    <token name="@DATASET_EXEMPLE2@">
+
++-------------+------------+------------+------------+
+| Hugo_Symbol | TCGAA62670 | TCGAA62671 | TCGAA62672 |
++=============+============+============+============+
+|    A1BG     |  0.523167  |  0.371355  |  0.925661  |
++-------------+------------+------------+------------+
+|    A1CF     |  0.568765  |  0.765567  |  0.456789  |
++-------------+------------+------------+------------+
+|     A2M     |  0.876545  |  0.768933  |  0.987654  |
++-------------+------------+------------+------------+
+|    A4GALT   |  0.456788  |  0.876543  |  0.876542  |
++-------------+------------+------------+------------+
+|   M664Y65   |  0.876543  |  0.786543  |  0.897654  |
++-------------+------------+------------+------------+
+
+|
+
+    </token>
+
+    <token name="@REFERENCE@">
+
+This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_. Development team: Irene Sala, Luca Rosato, Davide Maspero, Chiara Damiani.
+
+.. _BIMIB: http://sito di bio.org
+.. _Department of Informatics, Systems and Communications: http://www.disco.unimib.it/go/Home/English
+.. _University of Milan - Bicocca: https://www.unimib.it/
+
+    </token>
+
+    <xml name="citations">
+        <citations> <!--esempio di citazione-->
+            <citation type="bibtex">
+@online{lh32017,
+  author = {Alex Graudenzi, Davide Maspero, Cluadio Isella, Marzia Di Filippo, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani},
+  year = {2018},
+  title = {MaREA: Metabolic feature extraction, enrichment and visualization of RNAseq},
+  publisher = {bioRxiv},
+  journal = {bioRxiv},
+  url = {https://www.biorxiv.org/content/early/2018/01/16/248724},
+}
+            </citation>
+        </citations>
+    </xml>
+
+</macros>