# HG changeset patch
# User recetox
# Date 1598532938 0
# Node ID b5b62d04625a9be49f8a073ab556bf1fada9053e

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b9cf078bf1136d497d624b62eae7f56f58d1f03"

diff -r 000000000000 -r b5b62d04625a biotransformer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biotransformer.xml	Thu Aug 27 12:55:38 2020 +0000
@@ -0,0 +1,129 @@
+<tool id="biotransformer" name="BioTransformer" version="1.1.0">
+    <requirements>
+      <container type="docker">registry.gitlab.ics.muni.cz:443/recetox/mass-spectrometry/biotransformer:1.1.0</container>
+    </requirements>
+  <command><![CDATA[ cd /biotransformer && python3 wrapper_biotransformer.py
+ -k $k
+ -b $b 
+ -s $steps
+ -t $tolerance
+ -a
+ #if $input.type_selector == "sdf"
+	-isdf $input.input_format
+ #else if $input.type_selector == "csv"
+	-icsv $input.input_format
+ #else
+	-ismi "$input.input_format"
+ #end if
+
+ #if $output.type_selector == "csv"
+   #if $input.type_selector == "csv"
+	-ocsv $output_file
+        -ocsvDup $output_file2
+        -ocsvDup2 $output_file3	
+   #else if $input.type_selector == "smile"
+	-ocsv $output_file
+   #end if
+ #else
+	-osdf $output_file
+ #end if
+
+  ]]>
+  </command>
+  <inputs>
+    <param name="k" type="select" value="pred" label="The task to be permed [pred=prediction, cid=compound identification].">
+       <option value="pred" selected="true" >pred</option>
+       <option value="cid">cid</option>
+    </param>
+    <param name="b" type="select" value="ecbased" label="The type of description.">
+       <option value="ecbased" selected="true" >EC-based</option>
+       <option value="cyp450">CYP450</option>
+       <option value="phaseII">Phase II</option>
+       <option value="hgut">Human gut microbial</option>
+       <option value="superbio">Human super transformer 1 (superbio)</option>
+       <option value="allHuman">Human super transformer 2 (allHuman)</option>
+       <option value="envimicro">Environmental microbial</option>
+    </param>
+    <param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/>
+    <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/>
+
+    <conditional name="input">
+    	<param name="type_selector" type="select" label="Input format [SMILES, SDF, CSV].">
+        	<option value="smile" selected="true">SMILES</option>
+		<option value="sdf">SDF</option>
+		<option value="csv">CSV</option>
+        </param>
+        <when value="sdf">
+        	<param name="input_format" argument="-isdf" type="data" format="sdf" label="SDF"/>
+    	</when>
+    	<when value="smile">
+        	<param name="input_format" argument="-ismi" type="text" label="SMILES (example string format: CC(C)C1=CC=C(C)C=C1O )."/>
+    	</when>
+	<when value="csv">
+		<param name="input_format" argument="-csv" type="data" format="csv" label="CSV with one molecule (SMILES format) per line."/>
+	</when>
+    </conditional>
+
+    <conditional name="output">
+        <param name="type_selector" type="select" label="Output format [CSV, SDF].">
+                <option value="osdf" selected="true">SDF</option>
+                <option value="csv">CSV</option>
+        </param>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data format="csv" name="output_file" label="BioTransformer - output.">
+            <change_format>
+                <when input="output.type_selector" value="osdf" format="sdf" />
+            </change_format>
+    </data>
+    <data format="csv" name="output_file2" label="BioTransformer - filtered CSV output.">
+	  <filter>input['type_selector'] == 'csv'</filter>
+    </data>
+    <data format="csv" name="output_file3" label="BioTransformer - super-filtered CSV output.">
+	  <filter>input['type_selector'] == 'csv'</filter>
+    </data>
+  </outputs>
+  <help>
+BioTransformer is a software tool that predicts small molecule metabolism in mammals, their gut micr obiota,
+as well as the soil/aquatic microbiota. BioTransformer also assists scientists in metabolite identification,
+based on the metabolism prediction.
+
+BioTransformer is offered to the public as a freely acessible software package under the GNU License GPL v2.1.
+
+Users are free to copy and redistribute the material in any medium or format. Moreover, they could modify, and
+build upon the material under the condition that they must give appropriate credit, provide links to the license,
+and indicate if changes were made. Furthermore, the above copyright notice and this permission notice must be
+included. Use and re-distribution of the these resources, in whole or in part, for commercial purposes requires
+explicit permission of the authors. We ask that all users of the BioTransformer software tool, the BioTransformer
+web server, or BioTransformerDB to cite the BioTransformer reference in any resulting publications, and to
+acknowledge the authors.
+
+Parameters explanation:
+
+Input. User can chose from SDF, SMILES and CSV. CSV expects file with one moleluce in SMILES format per line. If CSV
+is selected, OUTPUT MUST BE CSV AS WELL!
+
+The type of description: Type of biotransformer - EC-based (ecbased), CYP450 (cyp450), Phase II (phaseII), Human gut
+microbial (hgut), human super transformer* (superbio, or allHuman), Environmental microbial (envimicro).
+
+The number of steps for the prediction. This option will be used for the EC-based, CYP450, Phase II, and Environmental
+microbial biotransformers. The default value is 1.
+
+Mass tolerance for metabolite identification (default is 0.01).
+
+Output of BioTransformer with CSV as an input are 3 CSV files. One without any filtering, second with filtered
+duplicates based on 6 columns (InChI, InChIKey, Synonyms, Molecular formula, Major Isotope Mass, AlogP) and third with
+filtered duplicates based on 3 columns (Molecular formula, Major Isotope Mass, AlogP).
+
+Output of BioTransformer with SMILES as an input is 1 CSV file.
+
+(* ) While the 'superbio' option runs a set number of transformation steps in a pre-defined order (e.g. deconjugation
+first, then Oxidation/reduction, etc.), the 'allHuman' option predicts all possible metabolites from any applicable
+reaction(Oxidation, reduction, (de-)conjugation) at each step.
+  </help>
+  <citations>
+    <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation>
+  </citations>
+</tool>