Mercurial > repos > recetox > retip_apply

comparison retip_apply.xml @ 9:a66070c7d55b draft default tip

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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
comparison
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8:eaccaebf11cb 9:a66070c7d55b
1 <tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy3"> 1 <tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy3">
2 <description>is retention time predictor for Metabolomics</description> 2 <description>is retention time predictor for Metabolomics</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="creator"/>
7
6 <expand macro="requirements"/> 8 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
8 #if $input_smiles.is_of_type('tabular') 10 #if $input_smiles.is_of_type('tabular')
9 /run.sh spell_tsv.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --name '$name_col' --smiles '$smiles_col' --out 'output_file' --bad 'bad_file' 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'
10 #else 12 #else
15 <inputs> 17 <inputs>
16 <param name="descr_train" label="Select Descriptors.h5 Dataset" type="data" format="h5" optional="false"/> 18 <param name="descr_train" label="Select Descriptors.h5 Dataset" type="data" format="h5" optional="false"/>
17 <param name="model_h5" label="Select Model.h5 Dataset" type="data" format="h5" optional="false"/> 19 <param name="model_h5" label="Select Model.h5 Dataset" type="data" format="h5" optional="false"/>
18 <param format="tabular,h5" name="input_smiles" type="data" label="Select Input Smiles tsv or h5 Dataset" 20 <param format="tabular,h5" name="input_smiles" type="data" label="Select Input Smiles tsv or h5 Dataset"
19 optional="false"/> 21 optional="false"/>
20 <param name="smiles_col" type="text" label="Name of input column with SMILES" optional="true" value="qsar_smiles"/> 22 <param name="smiles_col" type="text" label="Name of input column with SMILES" optional="true"
21 <param name="name_col" type="text" label="Name of input column with some unique identifier" optional="true" value="recetox_cid"/> 23 value="qsar_smiles"/>
22 <param name="ids" type="text" label="Input H5 dataset" optional="true" value="/annotations"/> 24 <param name="name_col" type="text" label="Name of input column with some unique identifier" optional="true"
23 <param name="ods" type="text" label="Output H5 dataset" optional="true" value="/annotations"/> 25 value="recetox_cid"/>
26 <param name="ids" type="text" label="Input H5 dataset" optional="true" value="/annotations"/>
27 <param name="ods" type="text" label="Output H5 dataset" optional="true" value="/annotations"/>
24 </inputs> 28 </inputs>
25 <outputs> 29 <outputs>
26 <data format_source="input_smiles" name="output_good" label="Predicted RT" from_work_dir="output_file"/> 30 <data format_source="input_smiles" name="output_good" label="Predicted RT" from_work_dir="output_file"/>
27 <data format_source="input_smiles" name="output_bad" label="Failed RT prediction" from_work_dir="bad_file"/> 31 <data format_source="input_smiles" name="output_bad" label="Failed RT prediction" from_work_dir="bad_file"/>
28 </outputs> 32 </outputs>
42 <param name="ods" value="/compounds"/> 46 <param name="ods" value="/compounds"/>
43 <output name="output_good" file="good.h5" ftype="h5" compare="sim_size" delta="50"/> 47 <output name="output_good" file="good.h5" ftype="h5" compare="sim_size" delta="50"/>
44 <output name="output_bad" file="bad.h5" ftype="h5" compare="sim_size" delta="50"/> 48 <output name="output_bad" file="bad.h5" ftype="h5" compare="sim_size" delta="50"/>
45 </test> 49 </test>
46 </tests> 50 </tests>
47 <help><![CDATA[ 51 <help>
48 .. class:: infomark 52 <![CDATA[
53 .. class:: infomark
49 54
50 This tool is used for **Retention Time Prediction** on a whole database. 55 This tool is used for **Retention Time Prediction** on a whole database.
51 56
52 @HELP@ 57 @HELP@
53 ]]> 58 ]]>
54 </help> 59 </help>
55 <expand macro="citations"/> 60 <expand macro="citations"/>
56 </tool> 61 </tool>