diff biotransformer.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/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>