<tool id="FluxToMap" name="Metabolic Flux Enrichment Analysis" version="2.0.0">
	<macros>
		<import>marea_macros.xml</import>
	</macros>
	
	<requirements>
		<requirement type="package" version="1.24.4">numpy</requirement>
        <requirement type="package" version="2.0.3">pandas</requirement>
		<requirement type="package" version="0.13.0">seaborn</requirement>
        <requirement type="package" version="1.10.1">scipy</requirement>
		<requirement type="package" version="1.5.1">svglib</requirement>
		<requirement type="package" version="2.2.3">pyvips</requirement>
		<requirement type="package" version="2.7.1">cairosvg</requirement>
		<requirement type="package" version="0.29.0">cobra</requirement>
		<requirement type="package" version="5.2.2">lxml</requirement>
	</requirements>
	
	<command detect_errors="exit_code">
		<![CDATA[
      	python $__tool_directory__/flux_to_map.py

      	--tool_dir $__tool_directory__
      	--option $cond.type_selector
        --out_log $log
		--color_map $color_map
	
        #if $cond.type_selector == 'datasets':

			--input_datas_fluxes
			#for $data in $cond.input_datasets_fluxes:
				${data.input_fluxes}
			#end for

			--names_fluxes
			#for $data in $cond.input_datasets_fluxes:
				${data.input_name_fluxes}
			#end for

        #elif $cond.type_selector == 'dataset_class':

			--input_data_fluxes $input_data_fluxes
			--input_class_fluxes $input_class_fluxes

        #end if

		--comparison ${comparis.comparison}
		#if $comparis.comparison == 'onevsmany'
			--control '${cond.comparis.controlgroup}'
		#end if

		--choice_map '${cond_choice_map.choice_map}'
		#if $cond_choice_map.choice_map == 'Custom':
			--custom_map ${cond_choice_map.custom_map}
		#end if
		
		#if $advanced.choice == 'true':
			--pValue ${advanced.pValue}
			--fChange ${advanced.fChange}
			--generate_svg ${advanced.generateSvg}
			--generate_pdf ${advanced.generatePdf}
		#else 
			--pValue 0.05
			--fChange 1.2
			--generate_svg false
			--generate_pdf true
		#end if
        ]]>
	</command>
	
	<inputs>

		<conditional name="cond">
			<param name="type_selector" argument="--option" type="select" label="Input format:">
				<option value="datasets" selected="true">Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N</option>
				<option value="dataset_class">All fluxes + sample group specification</option>
			</param>

			<when value="datasets">
				<repeat name="input_datasets_fluxes" title="Fluxes dataset" min="2">
					<param name="input_fluxes" argument="--input_datas_fluxes" type="data" format="tabular, csv, tsv" label="add dataset" />
					<param name="input_name_fluxes" argument="--names_fluxes" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" />
				</repeat>
			</when>

			<when value="dataset_class">
				<param name="input_data_fluxes" argument="--input_data_fluxes" type="data" format="tabular, csv, tsv" label="All fluxes" />
				<param name="input_class_fluxes" argument="--input_class_fluxes" type="data" format="tabular, csv, tsv" label="Sample group specification" />
			</when>
		</conditional>

		<conditional name="comparis">
			<param name="comparison" argument="--comparison" type="select" label="Groups comparison:">
				<option value="manyvsmany" selected="true">One vs One</option>
				<option value="onevsrest">One vs All</option>
				<option value="onevsmany">One vs Control</option>
			</param>
			<when value="onevsmany">
				<param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/>
			</when>
		</conditional>
		
		<conditional name="cond_choice_map">
			<param name="choice_map" argument="--choice_map" type="select" label="Choose metabolic map:">
				<option value="ENGRO2" selected="true">ENGRO2</option>
				<option value="HMRcore" >HMRcore</option>
				<option value="Custom">Custom</option>
			</param>

			<when value="Custom">				
				<param name="custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/>
			</when>
		</conditional>

		<param name="color_map" argument="--color_map" type="select" label="Color map:">
				<option value="viridis" selected="true">Viridis</option>
				<option value="jet">Jet</option>
		</param>

		<conditional name="advanced">
			<param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps.">
				<option value="true" selected="true">No</option>
				<option value="false">Yes</option>
			</param>

			<when value="true">
				<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="1.2" min="1" label="Fold-Change threshold:" help="min value 1" />
				<param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" />
				<param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" />
			</when>
		</conditional>
	</inputs>

	<outputs>
		<data format="txt" name="log" label="FluxToMap - Log" />
		<collection name="results" type="list" label="FluxToMap - Results">
			<discover_datasets pattern="__name_and_ext__" directory="result"/>
		</collection>
	</outputs>
	
	<help>
	<![CDATA[

What it does
-------------

This tool analyzes and visualizes differences in reactions fluxes of groups of samples, returned by the Flux Simulation tool, of groups of samples.

Accepted files are (Files must have different names): 
    - option 1) two or more fluxes datasets, each referring to samples in a given group. The user can specify a label for each group;
    - option 2) one fluxes dataset and one group-file specifying the group each sample belongs to (e.g. the accepted group file is thought to be the one returned by the Clustering tool).

Optional files:
    - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.

The tool generates:
    - A tab-separated file: reporting fold-change and p-values of fluxes between a pair of conditions/classes;
    - A metabolic map file (downloadable as .svg and .png): visualizing up- and down-regulated reactions between a pair of conditions/classes;
    - Two metabolic maps to visualize the mean and median fluxes normalized amongst all classes. The associated color map is also generated (absolute ranges);
    - A log file (.txt).

Output options:
	- To calculate P-Values and Fold-Changes and to enrich maps, comparisons are performed for each possible pair of groups (default option ‘One vs One’).

Alternative options are:
    - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
    - comparison of each group vs. a control group (option ‘One vs Control). If this option is selected the user must indicate the control group label.

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
-------------

"Fluxes of group 1 + Fluxes of group 2 + ... + Fluxes of group N" option:

Fluxes Dataset 1:

+------------+----------------+----------------+----------------+ 
| Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
+============+================+================+================+
| r1642      |    0.523167    |    0.371355    |    0.925661    |  
+------------+----------------+----------------+----------------+    
| r1643      |    0.568765    |    0.765567    |    0.456789    |    
+------------+----------------+----------------+----------------+    
| r1640      |    0.876545    |    0.768933    |    0.987654    |  
+------------+----------------+----------------+----------------+
| r1641      |    0.456788    |    0.876543    |    0.876542    |    
+------------+----------------+----------------+----------------+    
| r1646      |    0.876543    |    0.786543    |    0.897654    |   
+------------+----------------+----------------+----------------+

Fluxes Dataset 2:

+------------+----------------+----------------+----------------+ 
| Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
+============+================+================+================+
| r1642      |    0.523167    |    0.371355    |    0.925661    |  
+------------+----------------+----------------+----------------+    
| r1643      |    0.568765    |    0.765567    |    0.456789    |    
+------------+----------------+----------------+----------------+    
| r1640      |    0.876545    |    0.768933    |    0.987654    |  
+------------+----------------+----------------+----------------+
| r1641      |    0.456788    |    0.876543    |    0.876542    |    
+------------+----------------+----------------+----------------+    
| r1646      |    0.876543    |    0.786543    |    0.897654    |   
+------------+----------------+----------------+----------------+

"Fluxes of all samples + sample group specification" option:

Fluxes Dataset:

+------------+----------------+----------------+----------------+ 
| Reaction ID|   TCGAA62670   |   TCGAA62671   |   TCGAA62672   |  
+============+================+================+================+
| r1642      |    0.523167    |    0.371355    |    0.925661    |  
+------------+----------------+----------------+----------------+    
| r1643      |    0.568765    |    0.765567    |    0.456789    |    
+------------+----------------+----------------+----------------+    
| r1640      |    0.876545    |    0.768933    |    0.987654    |  
+------------+----------------+----------------+----------------+
| r1641      |    0.456788    |    0.876543    |    0.876542    |    
+------------+----------------+----------------+----------------+    
| r1646      |    0.876543    |    0.786543    |    0.897654    |   
+------------+----------------+----------------+----------------+

Group-file

+---------------+-----------+
| Patient ID    |   Class   | 
+===============+===========+
| TCGAAA3529    |    MSI    | 
+---------------+-----------+  
| TCGAA62671    |    MSS    |    
+---------------+-----------+   
| TCGAA62672    |    MSI    |
+---------------+-----------+


**TIP**: If your dataset is not split into classes, use MaREA cluster analysis.


]]>
	</help>
	<expand macro="citations" />
</tool>