Mercurial > repos > recetox > retip_apply

comparison retip_apply.xml @ 3:cb939f736490 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 880667785eed143b5d777010c79a12a53a00af4f"
author recetox
date Fri, 09 Oct 2020 08:54:34 +0000
parents 679229b50d4d
children c550dae786fd
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2:679229b50d4d 3:cb939f736490
1 <tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy2">
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="requirements"/> 6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 /run.sh spell.R '$descr_train' '$model_hdf5' '$input_smiles' 'output.tsv' 8 #if $input_smiles.is_of_type('tabular')
9 /run.sh spell.R '$descr_train' '$model_h5' '$input_smiles' 'output_file'
10 #else
11 /run.sh spell_h5.R '$descr_train' '$model_h5' '$input_smiles' 'output_file'
12 #end if
9 ]]> 13 ]]>
10 </command> 14 </command>
11 <inputs> 15 <inputs>
12 <param name="descr_train" label="Select Descriptors.h5 Dataset" type="data" format="h5" 16 <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"/>
18 <param format="tabular,h5" name="input_smiles" type="data" label="Select Input Smiles tsv or h5 Dataset"
13 optional="false"/> 19 optional="false"/>
14 <param name="model_hdf5" label="Select Model.h5 Dataset" type="data" format="h5" optional="false"/>
15 <param name="input_smiles" label="Select Input Dataset" type="data" format="tabular" optional="false"/>
16 </inputs> 20 </inputs>
17 <outputs> 21 <outputs>
18 <data format="tabular" name="output1" label="Predicted RT" from_work_dir="output.tsv"/> 22 <data format_source="input_smiles" name="output1" label="Predicted RT" from_work_dir="output_file"/>
19 </outputs> 23 </outputs>
20 <tests> 24 <tests>
21 <test expect_num_outputs="1"> 25 <test expect_num_outputs="1">
22 <param name="descr_train" value="descriptors.h5"/> 26 <param name="descr_train" value="descriptors.h5"/>
23 <param name="model_hdf5" value="model.h5"/> 27 <param name="model_h5" value="model.h5"/>
24 <param name="input_smiles" value="input.tsv"/> 28 <param name="input_smiles" value="input.tsv"/>
25 <output name="output1" file="output.tsv" ftype="tabular" compare="sim_size" delta="50"/> 29 <output name="output1" file="output.tsv" ftype="tabular" compare="sim_size" delta="50"/>
30 </test>
31 <test expect_num_outputs="1">
32 <param name="descr_train" value="descriptors.h5"/>
33 <param name="model_h5" value="model.h5"/>
34 <param name="input_smiles" value="input.h5"/>
35 <output name="output1" file="output.h5" ftype="h5" compare="sim_size" delta="50"/>
26 </test> 36 </test>
27 </tests> 37 </tests>
28 <help><![CDATA[ 38 <help><![CDATA[
29 .. class:: infomark 39 .. class:: infomark
30 40