# HG changeset patch
# User recetox
# Date 1614957588 0
# Node ID c550dae786fd6d7f95e39fa55849e706b7eb21ea
# Parent  0dfadbac4bed113c9c541781155f0a715dea5afd
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 683f472a44f296d65cf572a5e720839fc4c0141e-dirty"

diff -r 0dfadbac4bed -r c550dae786fd macros.xml
--- a/macros.xml	Thu Nov 05 09:21:43 2020 +0000
+++ b/macros.xml	Fri Mar 05 15:19:48 2021 +0000
@@ -2,7 +2,7 @@
     <token name="@TOOL_VERSION@">0.5.4</token>
     <xml name="requirements">
         <requirements>
-            <container type="docker">recetox/retip:@TOOL_VERSION@-recetox3</container>
+            <container type="docker">recetox/retip:@TOOL_VERSION@-recetox4</container>
         </requirements>
     </xml>
     <xml name="citations">
diff -r 0dfadbac4bed -r c550dae786fd retip_apply.xml
--- a/retip_apply.xml	Thu Nov 05 09:21:43 2020 +0000
+++ b/retip_apply.xml	Fri Mar 05 15:19:48 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy2">
+<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy3">
     <description>is retention time predictor for Metabolomics</description>
     <macros>
         <import>macros.xml</import>
@@ -6,9 +6,9 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
             #if $input_smiles.is_of_type('tabular')
-               /run.sh spell.R '$descr_train' '$model_h5' '$input_smiles' 'output_file'
+               /run.sh spell_tsv.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --out 'output_file' --bad 'bad_file'
             #else
-               /run.sh spell_h5.R '$descr_train' '$model_h5' '$input_smiles' 'output_file'
+               /run.sh spell_h5.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --out 'output_file' --bad 'bad_file'
             #end if
       ]]>
     </command>
@@ -17,22 +17,25 @@
         <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="smiles_col" type="text" label="Name of input column with SMILES" optional="true" value="qsar_smiles"/>
+	<param name="name_col" type="text" label="Name of input column with some unique identifier" optional="true" value="recetox_cid"/>
     </inputs>
     <outputs>
-        <data format_source="input_smiles" name="output1" label="Predicted RT" from_work_dir="output_file"/>
+        <data format_source="input_smiles" name="output_good" label="Predicted RT" from_work_dir="output_file"/>
+        <data format_source="input_smiles" name="output_bad" label="Predicted RT" from_work_dir="bad_file"/>
     </outputs>
     <tests>
         <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.tsv"/>
-            <output name="output1" file="output.tsv" ftype="tabular" compare="sim_size" delta="50"/>
+            <output name="output_good" 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"/>
+            <output name="output_good" file="output.h5" ftype="h5" compare="sim_size" delta="50"/>
         </test>
     </tests>
     <help><![CDATA[