comparison Marea/marea.xml @ 1:9e63d5f02d62 draft

Uploaded

0:23ac9cf12788

<tool id="MaREA" name="Metabolic Enrichment Analysis">
    <description>for Galaxy</description>
    <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>
        <![CDATA[
      	python $__tool_directory__/marea.py
        --rules_selector $cond_rule.rules_selector
        #if $cond_rule.rules_selector == 'Custom':
            --custom ${cond_rule.Custom_rules}

            --input_data ${input_data}
            --input_class ${input_class}
        #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>
            <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" type="data" format="xml, svg" label="custom-map.svg"/>
                    </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>
                <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"/>
	        </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"/>
            </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"/>
    </inputs>
    <outputs>
        <data format="txt" name="log" label="Log"/>
        <collection name="map_svg" type="list" label="file 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"/>
        </collection>
        <collection name="map_pdf" type="list" label="file 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"/>
        </collection>
        <collection name="table_out" type="list" label="file table">
            <discover_datasets pattern="__name_and_ext__" directory="table_out"/>
        </collection>
    </outputs>
    <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.

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: 
    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.


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


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

**"RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N" exemple input"** option:

Dataset 1:						

+------------+------------+------------+------------+   
|  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 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  |
+-------------+------------+------------+------------+

|

**"RNAseq of all samples + sample group specification"** option:

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  |   
+------------+------------+------------+------------+ 

|

Class-file:

+------------+------------+   
| Patient_ID |    class   |   

| TCGAA62672 |     MSI    |   
+------------+------------+

|



.. 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`_.

.. class:: infomark

TIP: If your dataset is not split into classes, use `Cluster for MaREA`_.

This tool is developed by the `nome del gruppo di bioinformatica`_ at the `dipartimento di informatica disco`_.


.. _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

]]>
    </help>
</tool>
	
	
	
	
	
	
	
	
	
	
	
	
	

1:9e63d5f02d62

<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">lxml</requirement>
        <requirement type="package">svglib</requirement>
        <requirement type="package">reportlab</requirement>
    </requirements>
    <command detect_errors="exit_code">
        <![CDATA[
      	python $__tool_directory__/marea.py
        --rules_selector $cond_rule.rules_selector
        #if $cond_rule.rules_selector == 'Custom':
            --custom ${cond_rule.Custom_rules}

            --input_data ${input_data}
            --input_class ${input_class}
        #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="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" 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" 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" 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="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" />
        </collection>
        <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" />
        </collection>
        <collection name="table_out" type="list" label="Tabular results">
            <discover_datasets pattern="__name_and_ext__" directory="table_out" />
        </collection>
    </outputs>

    

    <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   |   

| 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>