Mercurial > repos > recetox > biotransformer
diff biotransformer.xml @ 0:0b86600b715e draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
author | recetox |
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date | Tue, 06 Jun 2023 11:23:51 +0000 |
parents | |
children | 296bd426527f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biotransformer.xml Tue Jun 06 11:23:51 2023 +0000 @@ -0,0 +1,70 @@ +<tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy0" profile="21.09"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="creator"/> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">biotransformer</requirement> + <requirement type="package" version="3.1.1">openbabel</requirement> + <requirement type="package" version="1.1.1">pandas</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + python3 '${__tool_directory__}/wrapper_biotransformer.py' + -k $k + -b $b + -s $steps + -t $tolerance + -a + -icsv $input_file + -ocsv $output_file + -ocsvDup $output_file2 + -ocsvDup2 $output_file3 + ]]> + </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."/> + <param name="input_file" type="data" format="csv" label="Input CSV file."/> + </inputs> + + <outputs> + <data format="tsv" name="output_file" label="BioTransformer on ${on_string}"/> + <data format="tsv" name="output_file2" label="BioTransformer with filter on ${on_string}"/> + <data format="tsv" name="output_file3" label="BioTransformer with super filter on ${on_string}"/> + </outputs> + + <tests> + <test> + <param name="k" value="pred"/> + <param name="b" value="allHuman"/> + <param name="steps" value="1"/> + <param name="tolerance" value="0.01"/> + <param name="input_file" value="smiles.csv"/> + <output name="output_file" value="output1.tsv"/> + <output name="output_file2" value="output2.tsv"/> + <output name="output_file3" value="output3.tsv"/> + </test> + </tests> + <help> + <![CDATA[ + @HELP@ + ]]> + </help> + <citations> + <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation> + </citations> +</tool>