annotate biotransformer.xml @ 3:e5fcba090b10 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:24:26 +0000
parents 90dc951da294
children 6cd2a9e6ac49
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e5fcba090b10 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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1 <tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy2" profile="21.09">
0
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <expand macro="creator"/>
2
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6 <xrefs>
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7 <xref type="bio.tools">biotransformer</xref>
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8 </xrefs>
0
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9 <requirements>
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10 <requirement type="package" version="3.0_20230403">biotransformer</requirement>
0
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11 <requirement type="package" version="3.1.1">openbabel</requirement>
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12 <requirement type="package" version="1.1.1">pandas</requirement>
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13 </requirements>
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14 <command detect_errors="aggressive"><![CDATA[
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15 python3 '${__tool_directory__}/wrapper_biotransformer.py'
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16 -k $k
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17 -b $b
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18 -s $steps
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19 -t $tolerance
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20 -a
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21 -icsv $input_file
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22 -ocsv $output_file
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23 -ocsvDup $output_file2
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24 -ocsvDup2 $output_file3
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param name="k" type="select" value="pred"
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29 label="The task to be permed [pred=prediction, cid=compound identification].">
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30 <option value="pred" selected="true">pred</option>
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31 <option value="cid">cid</option>
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32 </param>
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33 <param name="b" type="select" value="ecbased" label="The type of description.">
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34 <option value="ecbased" selected="true">EC-based</option>
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35 <option value="cyp450">CYP450</option>
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36 <option value="phaseII">Phase II</option>
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37 <option value="hgut">Human gut microbial</option>
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38 <option value="superbio">Human super transformer 1 (superbio)</option>
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39 <option value="allHuman">Human super transformer 2 (allHuman)</option>
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40 <option value="envimicro">Environmental microbial</option>
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41 </param>
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42 <param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/>
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43 <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/>
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44 <param name="input_file" type="data" format="csv" label="Input CSV file."/>
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45 </inputs>
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46
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47 <outputs>
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48 <data format="tsv" name="output_file" label="BioTransformer on ${on_string}"/>
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49 <data format="tsv" name="output_file2" label="BioTransformer with filter on ${on_string}"/>
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50 <data format="tsv" name="output_file3" label="BioTransformer with super filter on ${on_string}"/>
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51 </outputs>
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52
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53 <tests>
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54 <test>
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55 <param name="k" value="pred"/>
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56 <param name="b" value="allHuman"/>
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57 <param name="steps" value="1"/>
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58 <param name="tolerance" value="0.01"/>
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59 <param name="input_file" value="smiles.csv"/>
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60 <output name="output_file">
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61 <assert_contents>
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62 <has_size value="8600" delta="300"/>
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63 <has_n_lines n="225" delta="10"/>
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64 </assert_contents>
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65 </output>
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66 <output name="output_file2">
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67 <assert_contents>
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68 <has_size value="8600" delta="300"/>
1
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69 <has_n_lines n="225" delta="10"/>
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70 </assert_contents>
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71 </output>
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72 <output name="output_file3">
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73 <assert_contents>
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74 <has_size value="7400" delta="300"/>
1
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75 <has_n_lines n="186" delta="10"/>
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76 </assert_contents>
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77 </output>
0
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78 </test>
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79 </tests>
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80 <help>
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81 <![CDATA[
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82 @HELP@
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83 ]]>
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84 </help>
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85 <citations>
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86 <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation>
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87 </citations>
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88 </tool>