# HG changeset patch
# User francesco_lapi
# Date 1747752620 0
# Node ID 4f5c45de593613d8d49511538075ce5678db0c51
# Parent  89f0a211d79dd2521ad7f675a6b8bc9c9ef9f113
Uploaded

diff -r 89f0a211d79d -r 4f5c45de5936 flux_to_map.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flux_to_map.xml	Tue May 20 14:50:20 2025 +0000
@@ -0,0 +1,257 @@
+<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 $comparis.comparison == 'onevsmany'
+			--control '${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':
+			--test ${advanced.test}
+			--pValue ${advanced.pValue}
+			--adjusted ${advanced.adjusted}
+			--fChange ${advanced.fChange}
+			--generate_svg ${advanced.generateSvg}
+			--generate_pdf ${advanced.generatePdf}
+		#else 
+			--test 'ks'
+			--pValue 0.05
+			--adjusted false
+			--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: statistical test, 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="test" argument="--test" type="select" label="Statistical test to use" help="Select the statistical test to use for the analysis based on your data and the amount of replicates. Paired T-test and Wilcoxon need the same number of replicates in each group.">
+					<option value="ks" selected="true">Kolmogorov-Smirnov</option>
+					<option value="ttest_p">T-test (paired)</option>
+					<option value="ttest_ind">T-test (unpaired)</option>
+					<option value="wilcoxon">Wilcoxon</option>
+					<option value="mw">Mann-Whitney</option>
+				</param>
+				<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="adjusted" argument="--adjusted" type="boolean" checked="false" label="Use adjusted p-values" help="Should the program adjust the P-values based on the FDR (Benjamini-Hochberg) correction?" />
+				<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>
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