Mercurial > repos > bimib > marea

--- a/ras_generator.xml	Wed Jan 22 11:45:41 2020 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,172 +0,0 @@
-<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>
-