Mercurial > repos > bimib > marea

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ras_generator.xml	Wed Jan 22 11:45:41 2020 -0500
@@ -0,0 +1,172 @@
+<tool id="MaREA RAS Generator" name="RAS Generator" version="1.0.0">
+    <description></description>
+    <macros>
+        <import>marea_macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="0.23.0">pandas</requirement>
+        <requirement type="package" version="1.1.0">scipy</requirement>
+        <requirement type="package" version="0.10.1">cobra</requirement>
+        <requirement type="package" version="4.2.1">lxml</requirement>
+        <requirement type="package" version="0.8.1">svglib</requirement>
+        <requirement type="package" version="3.4.0">reportlab</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+        <![CDATA[
+      	python $__tool_directory__/marea.py
+        --rules_selector $cond_rule.rules_selector
+      	--tool_dir $__tool_directory__
+      	--option $cond.type_selector
+        --out_log $log
+        --input_datas ${input_Datasets}
+        --single_ras_file $ras_single
+        --none ${cond.None}
+        #end if
+        ]]>
+    </command>
+
+    <inputs>
+        <conditional name="cond_rule">
+            <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" />
+                <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>
+        <conditional name="cond">
+
+             <param name="input_Datasets" 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="Default: Dataset" />
+                <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" />
+
+
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="log" label="MaREA - Log" />
+        <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}">
+        	<filter>cond['type_selector'] == "datasets_rasonly"</filter>
+        </data>
+        <collection name="results" type="list" label="MaREA - Results">
+        <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter>
+            <discover_datasets pattern="__name_and_ext__" directory="result"/>
+        </collection>
+	<collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular">
+	    <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter>
+    	    <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/>
+	</collection>
+
+    </outputs>
+    <tests>
+        <test>
+            <param name="pValue" value="0.56"/>
+            <output name="log" file="log.txt"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+What it does
+-------------
+
+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.
+
+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:
+
+	* (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.
+
+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".
+
+
+Example input
+-------------
+
+**"Custom Rules"** option:
+
+Custom Rules Dastaset:
+
+@CUSTOM_RULES_EXEMPLE@
+
+**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N"** option:
+
+RNA-seq Dataset 1:
+
+@DATASET_EXEMPLE1@
+
+RNA-seq Dataset 2:
+
+@DATASET_EXEMPLE2@
+
+**"RNAseq of all samples + sample group specification"** option:
+
+RNA-seq Dataset:
+
+@DATASET_EXEMPLE1@
+
+Class-file:
+
++------------+------------+
+| Patient_ID |    class   |
++============+============+
+| TCGAAA3529 |     MSI    |
++------------+------------+
+| TCGAA62671 |     MSS    |
++------------+------------+
+| TCGAA62672 |     MSI    |
++------------+------------+
+
+|
+
+.. class:: infomark
+
+**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 `MaREA cluster analysis`_.
+
+@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
+.. _MaREA cluster analysis: http://link del tool di cluster.org
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
+