Mercurial > repos > recetox > retip_apply

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:28:38 +0000
parents eaccaebf11cb
children
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1 <tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy3">
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2 <description>is retention time predictor for Metabolomics</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
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7
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #if $input_smiles.is_of_type('tabular')
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11 /run.sh spell_tsv.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --name '$name_col' --smiles '$smiles_col' --out 'output_file' --bad 'bad_file'
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12 #else
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13 /run.sh spell_h5.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --ids '$ids' --ods '$ods' --name '$name_col' --smiles '$smiles_col' --out 'output_file' --bad 'bad_file'
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14 #end if
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="descr_train" label="Select Descriptors.h5 Dataset" type="data" format="h5" optional="false"/>
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19 <param name="model_h5" label="Select Model.h5 Dataset" type="data" format="h5" optional="false"/>
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20 <param format="tabular,h5" name="input_smiles" type="data" label="Select Input Smiles tsv or h5 Dataset"
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21 optional="false"/>
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22 <param name="smiles_col" type="text" label="Name of input column with SMILES" optional="true"
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23 value="qsar_smiles"/>
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24 <param name="name_col" type="text" label="Name of input column with some unique identifier" optional="true"
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25 value="recetox_cid"/>
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26 <param name="ids" type="text" label="Input H5 dataset" optional="true" value="/annotations"/>
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27 <param name="ods" type="text" label="Output H5 dataset" optional="true" value="/annotations"/>
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28 </inputs>
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29 <outputs>
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30 <data format_source="input_smiles" name="output_good" label="Predicted RT" from_work_dir="output_file"/>
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31 <data format_source="input_smiles" name="output_bad" label="Failed RT prediction" from_work_dir="bad_file"/>
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32 </outputs>
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33 <tests>
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34 <test expect_num_outputs="2">
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35 <param name="descr_train" value="descriptors.h5"/>
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36 <param name="model_h5" value="model.h5"/>
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37 <param name="input_smiles" value="pubchem-99.tsv"/>
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38 <output name="output_good" file="pubchem-good.tsv" ftype="tabular"/>
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39 <output name="output_bad" file="pubchem-bad.tsv" ftype="tabular"/>
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40 </test>
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41 <test expect_num_outputs="2">
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42 <param name="descr_train" value="descriptors.h5"/>
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43 <param name="model_h5" value="model.h5"/>
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44 <param name="input_smiles" value="input.h5"/>
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45 <param name="ids" value="/compounds/table"/>
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46 <param name="ods" value="/compounds"/>
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47 <output name="output_good" file="good.h5" ftype="h5" compare="sim_size" delta="50"/>
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48 <output name="output_bad" file="bad.h5" ftype="h5" compare="sim_size" delta="50"/>
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49 </test>
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50 </tests>
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51 <help>
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52 <![CDATA[
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53 .. class:: infomark
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54
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55 This tool is used for **Retention Time Prediction** on a whole database.
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56
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57 @HELP@
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58 ]]>
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59 </help>
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60 <expand macro="citations"/>
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61 </tool>