Mercurial > repos > recetox > biotransformer
annotate biotransformer.xml @ 2:90dc951da294 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 038d752ab3a1eb53f9599f219da97faaa67bf08d
author | recetox |
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date | Fri, 23 Jun 2023 10:06:59 +0000 |
parents | 296bd426527f |
children | e5fcba090b10 |
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296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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1 <tool id="biotransformer" name="BioTransformer" version="@TOOL_VERSION@+galaxy1" profile="21.09"> |
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0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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2 <macros> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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3 <import>macros.xml</import> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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4 </macros> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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5 <expand macro="creator"/> |
2
90dc951da294
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 038d752ab3a1eb53f9599f219da97faaa67bf08d
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6 <xrefs> |
90dc951da294
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 038d752ab3a1eb53f9599f219da97faaa67bf08d
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7 <xref type="bio.tools">biotransformer</xref> |
90dc951da294
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 038d752ab3a1eb53f9599f219da97faaa67bf08d
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8 </xrefs> |
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0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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9 <requirements> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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10 <requirement type="package" version="@TOOL_VERSION@">biotransformer</requirement> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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11 <requirement type="package" version="3.1.1">openbabel</requirement> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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12 <requirement type="package" version="1.1.1">pandas</requirement> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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13 </requirements> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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14 <command detect_errors="aggressive"><![CDATA[ |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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15 python3 '${__tool_directory__}/wrapper_biotransformer.py' |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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16 -k $k |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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17 -b $b |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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18 -s $steps |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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19 -t $tolerance |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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20 -a |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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21 -icsv $input_file |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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22 -ocsv $output_file |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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23 -ocsvDup $output_file2 |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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24 -ocsvDup2 $output_file3 |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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25 ]]> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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26 </command> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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27 <inputs> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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28 <param name="k" type="select" value="pred" |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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29 label="The task to be permed [pred=prediction, cid=compound identification]."> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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30 <option value="pred" selected="true">pred</option> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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31 <option value="cid">cid</option> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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32 </param> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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33 <param name="b" type="select" value="ecbased" label="The type of description."> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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34 <option value="ecbased" selected="true">EC-based</option> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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35 <option value="cyp450">CYP450</option> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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36 <option value="phaseII">Phase II</option> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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37 <option value="hgut">Human gut microbial</option> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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38 <option value="superbio">Human super transformer 1 (superbio)</option> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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39 <option value="allHuman">Human super transformer 2 (allHuman)</option> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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40 <option value="envimicro">Environmental microbial</option> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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41 </param> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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42 <param name="steps" type="integer" value="1" label=" The number of steps for the prediction."/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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43 <param name="tolerance" type="float" value="0.01" label="Mass tolerance for metabolite identification."/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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44 <param name="input_file" type="data" format="csv" label="Input CSV file."/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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45 </inputs> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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46 |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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47 <outputs> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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48 <data format="tsv" name="output_file" label="BioTransformer on ${on_string}"/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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49 <data format="tsv" name="output_file2" label="BioTransformer with filter on ${on_string}"/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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50 <data format="tsv" name="output_file3" label="BioTransformer with super filter on ${on_string}"/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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51 </outputs> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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52 |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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53 <tests> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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54 <test> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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55 <param name="k" value="pred"/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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56 <param name="b" value="allHuman"/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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57 <param name="steps" value="1"/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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58 <param name="tolerance" value="0.01"/> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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59 <param name="input_file" value="smiles.csv"/> |
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296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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60 <output name="output_file"> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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61 <assert_contents> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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62 <has_size value="8600" delta="100"/> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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63 <has_n_lines n="225" delta="10"/> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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64 </assert_contents> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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65 </output> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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66 <output name="output_file2"> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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67 <assert_contents> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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68 <has_size value="8600" delta="100"/> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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69 <has_n_lines n="225" delta="10"/> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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70 </assert_contents> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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71 </output> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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72 <output name="output_file3"> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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73 <assert_contents> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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74 <has_size value="7400" delta="100"/> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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75 <has_n_lines n="186" delta="10"/> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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76 </assert_contents> |
296bd426527f
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 4083dcac523ed229543c802acbe1e8d2ffa46358
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77 </output> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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78 </test> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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79 </tests> |
0b86600b715e
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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80 <help> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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81 <![CDATA[ |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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82 @HELP@ |
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83 ]]> |
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84 </help> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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85 <citations> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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86 <citation type="doi">https://doi.org/10.1186/s13321-018-0324-5</citation> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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87 </citations> |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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88 </tool> |