Mercurial > repos > recetox > retip_apply

changeset 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 d59ce34543a4
files macros.xml retip_apply.xml test-data/input.h5 test-data/input_rt_filter.h5 test-data/output.h5 test-data/output_rt_filter.h5
diffstat 6 files changed, 18 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Oct 05 13:56:55 2020 +0000
+++ b/macros.xml	Fri Oct 09 08:54:34 2020 +0000
@@ -2,7 +2,7 @@
     <token name="@TOOL_VERSION@">0.5.4</token>
     <xml name="requirements">
         <requirements>
-            <container type="docker">recetox/retip:@TOOL_VERSION@-recetox1</container>
+            <container type="docker">recetox/retip:@TOOL_VERSION@-recetox2</container>
         </requirements>
     </xml>
     <xml name="citations">
--- a/retip_apply.xml	Mon Oct 05 13:56:55 2020 +0000
+++ b/retip_apply.xml	Fri Oct 09 08:54:34 2020 +0000
@@ -1,29 +1,39 @@
-<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy1">
+<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy2">
     <description>is retention time predictor for Metabolomics</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-           /run.sh spell.R '$descr_train' '$model_hdf5' '$input_smiles' 'output.tsv'
+            #if $input_smiles.is_of_type('tabular')
+               /run.sh spell.R '$descr_train' '$model_h5' '$input_smiles' 'output_file'
+            #else
+               /run.sh spell_h5.R '$descr_train' '$model_h5' '$input_smiles' 'output_file'
+            #end if
       ]]>
     </command>
     <inputs>
-        <param name="descr_train" label="Select Descriptors.h5 Dataset" type="data" format="h5"
+        <param name="descr_train" label="Select Descriptors.h5 Dataset" type="data" format="h5" optional="false"/>
+        <param name="model_h5" label="Select Model.h5 Dataset" type="data" format="h5" optional="false"/>
+        <param format="tabular,h5" name="input_smiles" type="data" label="Select Input Smiles tsv or h5 Dataset"
                optional="false"/>
-        <param name="model_hdf5" label="Select Model.h5 Dataset" type="data" format="h5" optional="false"/>
-        <param name="input_smiles" label="Select Input Dataset" type="data" format="tabular" optional="false"/>
     </inputs>
     <outputs>
-        <data format="tabular" name="output1" label="Predicted RT" from_work_dir="output.tsv"/>
+        <data format_source="input_smiles" name="output1" label="Predicted RT" from_work_dir="output_file"/>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
             <param name="descr_train" value="descriptors.h5"/>
-            <param name="model_hdf5" value="model.h5"/>
+            <param name="model_h5" value="model.h5"/>
             <param name="input_smiles" value="input.tsv"/>
             <output name="output1" file="output.tsv" ftype="tabular" compare="sim_size" delta="50"/>
         </test>
+        <test expect_num_outputs="1">
+            <param name="descr_train" value="descriptors.h5"/>
+            <param name="model_h5" value="model.h5"/>
+            <param name="input_smiles" value="input.h5"/>
+            <output name="output1" file="output.h5" ftype="h5" compare="sim_size" delta="50"/>
+        </test>
     </tests>
     <help><![CDATA[
 .. class:: infomark
Binary file test-data/input.h5 has changed
Binary file test-data/input_rt_filter.h5 has changed
Binary file test-data/output.h5 has changed
Binary file test-data/output_rt_filter.h5 has changed