Mercurial > repos > bimib > marea_2_0

changeset 183:cbe1cb0a55be draft

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Uploaded
author luca_milaz
date Thu, 04 Jul 2024 14:11:55 +0000
parents 7be7ea5283cb
children 88cf0882e175
files marea_2_0/flux_sampling.xml marea_2_0/statistics.xml
diffstat 2 files changed, 0 insertions(+), 172 deletions(-) [+]
line wrap: on
line diff
--- a/marea_2_0/flux_sampling.xml	Thu Jul 04 14:09:24 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,97 +0,0 @@
-<tool id="fluxSampling" name="COBRAxy Model sampling" version="2.0.0">
-    
-    <macros>
-        <import>marea_macros.xml</import>
-    </macros>
-
-	<requirements>
-        <requirement type="package" version="0.29.0">cobra</requirement>
-        <requirement type="package" version="4.9.3">lxml</requirement>
-        <requirement type="package" version="1.4.2">joblib</requirement>
-        
-	</requirements>
-
-    <command detect_errors="exit_code">
-        <![CDATA[
-        python $__tool_directory__/flux_sampling.py
-        --tool_dir $__tool_directory__
-        --input "${",".join(map(str, $inputs))}"
-        #set $names = ""
-        #for $input_temp in $inputs:
-            #set $names = $names + $input_temp.element_identifier + ","
-        #end for
-        --name $names
-        --thinning 0
-        #if $algorithm_param.algorithm == 'OPTGP':
-        	--thinning $algorithm_param.thinning
-        #end if
-        --algorithm $algorithm_param.algorithm
-        --n_batches $n_batches
-        --n_samples $n_samples
-        --seed $seed
-        --output_format $output_format
-        --out_log $log
-        ]]>
-    </command>
-    <inputs>
-
-        <param name="inputs" argument="--inputs" multiple="true" type="data" format="xml, json" label="Model(s):" />
-
-        <conditional name="algorithm_param">
-			<param name="algorithm" argument="--algorithm" type="select" label="Choose sampling algorithm:">
-                    <option value="CBS" selected="true">CBS</option>
-                	<option value="OPTGP">OPTGP</option>
-        	</param>
-        	<when value="OPTGP">
-        		<param name="thinning" argument="--thinning" type="integer" label="Thinning:"  value="100" help="Number of iterations to wait before taking a sample."/>
-        	</when>
-
-		</conditional>
-
-
-        <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" value="1000"/>
-
-        <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" value="1" help="The output file will contain n_batches*n_samples samples. 
-        This is useful for computational perfomances."/>
-
-        <param name="seed" argument="--seed" type="integer" label="Seed:" value="0" helph="Random seed."/>
-        
-        <param name="output_format" argument="--output_format" type="select" label="Output files format:">
-            <option value="pickle" selected="true">pickle extension (binary, non-editable, pre-parsed)</option>
-            <option value="csv">Comma Separated Values (csv text file, editable, raw)</option>
-        </param>
-    </inputs>
-
-        		
-    <outputs>
-        <data format="txt" name="log" label="fluxSampling - Log" />
-        <collection name="results" type="list" label="${tool.name} - Samples">
-            <discover_datasets pattern="__name_and_ext__" directory="flux_sampling"/>
-        </collection>
-    </outputs>
-       
-        
-    <help>
-    <![CDATA[
-What it does
--------------
-
-This tool generates flux samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) and OPTGP (mproved Artificial Centering Hit-and-Run sampler) sampling algorithms.
-
-Accepted files:
-    - A model: JSON or XML file reporting reactions and rules contained in the model. It can be a single model, multiple models or a collection of models. 
-
-Output:
--------------
-
-The tool generates:
-    - Samples: reporting the sampled fluxes for each reaction. Format: csv or pickle.
-    - a log file (.txt).
-
-**TIP**: The Batches parameter is useful to mantain in memory just a batch of samples at time. For example, if you wish to sample 10.000 points, than it is suggested to select n_samples = 1.000 and n_batches=10.
-
-
-]]>
-    </help>
-    <expand macro="citations" />
-</tool>
\ No newline at end of file
--- a/marea_2_0/statistics.xml	Thu Jul 04 14:09:24 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,75 +0,0 @@
-<tool id="statistics" name="Statistics" version="2.0.0">
-    
-    <macros>
-        <import>marea_macros.xml</import>
-    </macros>
-
-	<requirements>
-        <requirement type="package" version="0.29.0">cobra</requirement>
-        <requirement type="package" version="4.9.3">lxml</requirement>
-        <requirement type="package" version="1.4.2">joblib</requirement>
-        
-	</requirements>
-
-    <command detect_errors="exit_code">
-        <![CDATA[
-        python $__tool_directory__/statistics.py
-        --tool_dir $__tool_directory__
-        --input "${",".join(map(str, $inputs))}"
-        #set $names = ""
-        #for $input_temp in $inputs:
-            #set $names = $names + $input_temp.element_identifier + ","
-        #end for
-        --name $names
-        --statistics "${",".join(map(str, $statistics))}"
-        --toMerge toMerge
-        --out_log $log
-        ]]>
-    </command>
-    <inputs>
-
-        <param name="inputs" argument="--inputs" multiple="true" type="data" format="tabular, csv, tsv, p" label="Dataset(s):" />
-
-        <param type="select" argument="--statistics" multiple="true" name="statistics" label="Statistics">
-            <option value="mean" selected="true">Mean</option>
-            <option value="median">Median</option>
-            <option value="quantiles">Quantiles</option>
-            <option value="correlation">Biomass correlation</option>
-        </param>
-        <param name="toMerge" argument="--toMerge" type="boolean" checked="true" truevalue="Yes" falsevalue="No"
-         label="Merge datasets" help="If true, generate for each statiscs a single dataset having as index all the input datasets."/>
-    </inputs>
-
-        		
-    <outputs>
-        <data format="txt" name="log" label="statistics - Log" />
-        <collection name="results" type="list" label="${tool.name} - Statistics">
-            <discover_datasets pattern="__name_and_ext__" directory="statistics"/>
-        </collection>
-    </outputs>
-       
-        
-    <help>
-    <![CDATA[
-What it does
--------------
-
-This tool generates flux samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) and OPTGP (mproved Artificial Centering Hit-and-Run sampler) sampling algorithms.
-
-Accepted files:
-    - A model: JSON or XML file reporting reactions and rules contained in the model. It can be a single model, multiple models or a collection of models. 
-
-Output:
--------------
-
-The tool generates:
-    - Samples: reporting the sampled fluxes for each reaction. Format: csv or pickle.
-    - a log file (.txt).
-
-**TIP**: The Batches parameter is useful to mantain in memory just a batch of samples at time. For example, if you wish to sample 10.000 points, than it is suggested to select n_samples = 1.000 and n_batches=10.
-
-
-]]>
-    </help>
-    <expand macro="citations" />
-</tool>
\ No newline at end of file