diff macros.xml @ 0:0b86600b715e draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Jun 06 11:23:51 2023 +0000
@@ -0,0 +1,57 @@
+<macros>
+    <token name="@TOOL_VERSION@">3.0_20230403</token>
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Martin"
+                familyName="Čech"
+                url="https://github.com/martenson"
+                identifier="0000-0002-9318-1781" />
+            <person
+                givenName="Karolína"
+                familyName="Trachtová"
+                url="https://github.com/trachtok" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="[e-mail]"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+    <token name="@HELP@">
+        <![CDATA[
+            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 v3.
+
+            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.** Currently, only a CSV file with one SMILES per line is accepted.
+
+            **The type of prediction:** 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 TSV 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).
+
+            (* ) 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.
+        ]]>
+    </token>
+</macros>