view biotransformer.xml @ 0:b5b62d04625a draft

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

<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>