Mercurial > repos > recetox > retip_apply

diff retip_apply.xml @ 8:eaccaebf11cb draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/retip commit 66741485c24076df17e4a87bdaa53ec04d1c8792"
author recetox
date Tue, 09 Mar 2021 18:29:03 +0000
parents a93b84244cb7
children a66070c7d55b
line wrap: on
line diff
--- a/retip_apply.xml	Mon Mar 08 15:34:26 2021 +0000
+++ b/retip_apply.xml	Tue Mar 09 18:29:03 2021 +0000
@@ -6,9 +6,9 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
             #if $input_smiles.is_of_type('tabular')
-               /run.sh spell_tsv.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --out 'output_file' --bad 'bad_file'
+               /run.sh spell_tsv.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --name '$name_col' --smiles '$smiles_col' --out 'output_file' --bad 'bad_file'
             #else
-               /run.sh spell_h5.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --out 'output_file' --bad 'bad_file'
+               /run.sh spell_h5.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --ids '$ids' --ods '$ods' --name '$name_col' --smiles '$smiles_col' --out 'output_file' --bad 'bad_file'
             #end if
       ]]>
     </command>
@@ -19,23 +19,29 @@
                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"/>
+	<param name="ids" type="text" label="Input H5 dataset" optional="true" value="/annotations"/>
+	<param name="ods" type="text" label="Output H5 dataset" optional="true" value="/annotations"/>
     </inputs>
     <outputs>
         <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="Failed RT prediction" from_work_dir="bad_file"/>
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="2">
             <param name="descr_train" value="descriptors.h5"/>
             <param name="model_h5" value="model.h5"/>
-            <param name="input_smiles" value="input.tsv"/>
-            <output name="output_good" file="output.tsv" ftype="tabular" compare="sim_size" delta="50"/>
+            <param name="input_smiles" value="pubchem-99.tsv"/>
+            <output name="output_good" file="pubchem-good.tsv" ftype="tabular"/>
+            <output name="output_bad" file="pubchem-bad.tsv" ftype="tabular"/>
         </test>
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="2">
             <param name="descr_train" value="descriptors.h5"/>
             <param name="model_h5" value="model.h5"/>
             <param name="input_smiles" value="input.h5"/>
-            <output name="output_good" file="output.h5" ftype="h5" compare="sim_size" delta="50"/>
+            <param name="ids" value="/compounds/table"/>
+            <param name="ods" value="/compounds"/>
+            <output name="output_good" file="good.h5" ftype="h5" compare="sim_size" delta="50"/>
+            <output name="output_bad" file="bad.h5" ftype="h5" compare="sim_size" delta="50"/>
         </test>
     </tests>
     <help><![CDATA[