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annotate retip_apply.xml @ 6:c550dae786fd draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 683f472a44f296d65cf572a5e720839fc4c0141e-dirty"
author recetox
date Fri, 05 Mar 2021 15:19:48 +0000
parents cb939f736490
children a93b84244cb7
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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="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if $input_smiles.is_of_type('tabular')
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9 /run.sh spell_tsv.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --out 'output_file' --bad 'bad_file'
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10 #else
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11 /run.sh spell_h5.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --out 'output_file' --bad 'bad_file'
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12 #end if
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param name="descr_train" label="Select Descriptors.h5 Dataset" type="data" format="h5" optional="false"/>
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17 <param name="model_h5" label="Select Model.h5 Dataset" type="data" format="h5" optional="false"/>
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18 <param format="tabular,h5" name="input_smiles" type="data" label="Select Input Smiles tsv or h5 Dataset"
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19 optional="false"/>
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20 <param name="smiles_col" type="text" label="Name of input column with SMILES" optional="true" value="qsar_smiles"/>
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21 <param name="name_col" type="text" label="Name of input column with some unique identifier" optional="true" value="recetox_cid"/>
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22 </inputs>
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23 <outputs>
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24 <data format_source="input_smiles" name="output_good" label="Predicted RT" from_work_dir="output_file"/>
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25 <data format_source="input_smiles" name="output_bad" label="Predicted RT" from_work_dir="bad_file"/>
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26 </outputs>
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27 <tests>
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28 <test expect_num_outputs="1">
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29 <param name="descr_train" value="descriptors.h5"/>
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30 <param name="model_h5" value="model.h5"/>
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31 <param name="input_smiles" value="input.tsv"/>
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32 <output name="output_good" file="output.tsv" ftype="tabular" compare="sim_size" delta="50"/>
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33 </test>
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34 <test expect_num_outputs="1">
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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="input.h5"/>
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38 <output name="output_good" file="output.h5" ftype="h5" compare="sim_size" delta="50"/>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 .. class:: infomark
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44 This tool is used for **Retention Time Prediction** on a whole database.
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45
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46 @HELP@
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47 ]]>
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48 </help>
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49 <expand macro="citations"/>
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50 </tool>