diff model_prediction.xml @ 9:4aa701f5a393 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"

--- a/model_prediction.xml	Thu Oct 01 20:35:52 2020 +0000
+++ b/model_prediction.xml	Tue Apr 13 18:00:54 2021 +0000
@@ -1,11 +1,11 @@
-<tool id="model_prediction" name="Model Prediction" version="@VERSION@">
+<tool id="model_prediction" name="Model Prediction" version="@VERSION@" profile="20.05">
     <description>predicts on new data using a preffited model</description>
     <macros>
         <import>main_macros.xml</import>
         <import>keras_macros.xml</import>
     </macros>
-    <expand macro="python_requirements"/>
-    <expand macro="macro_stdio"/>
+    <expand macro="python_requirements" />
+    <expand macro="macro_stdio" />
     <version_command>echo "@VERSION@"</version_command>
     <command>
         <![CDATA[
@@ -29,8 +29,8 @@
         <inputs name="inputs" />
     </configfiles>
     <inputs>
-        <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object"/>
-        <param name="infile_weights" type="data" format="h5" optional="true" label="Choose the dataset containing weights for the estimator above" help="Optional. For deep learning only."/>
+        <param name="infile_estimator" type="data" format="zip" label="Choose the dataset containing pipeline/estimator object" />
+        <param name="infile_weights" type="data" format="h5" optional="true" label="Choose the dataset containing weights for the estimator above" help="Optional. For deep learning only." />
         <param argument="method" type="select" label="Select invocation method">
             <option value="predict" selected="true">predict</option>
             <option value="predict_proba">predict_proba</option>
@@ -43,17 +43,17 @@
                 <option value="variant_effect">reference genome and variant call file</option>
             </param>
             <when value="tabular">
-                <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/>
+                <param name="infile1" type="data" format="tabular" label="Training samples dataset:" />
                 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
                 <conditional name="column_selector_options_1">
-                    <expand macro="samples_column_selector_options" multiple="true"/>
+                    <expand macro="samples_column_selector_options" multiple="true" />
                 </conditional>
             </when>
             <when value="sparse">
-                <param name="infile1" type="data" format="txt" label="Select a sparse matrix" help=""/>
+                <param name="infile1" type="data" format="txt" label="Select a sparse matrix" help="" />
             </when>
             <when value="seq_fasta">
-                <param name="fasta_path" type="data" format="fasta" label="Dataset containing fasta genomic/protein sequences" help="Sequences will be one-hot encoded to arrays."/>
+                <param name="fasta_path" type="data" format="fasta" label="Dataset containing fasta genomic/protein sequences" help="Sequences will be one-hot encoded to arrays." />
                 <param name="seq_type" type="select" label="Sequence type">
                     <option value="FastaDNABatchGenerator">DNA</option>
                     <option value="FastaRNABatchGenerator">RNA</option>
@@ -61,45 +61,45 @@
                 </param>
             </when>
             <when value="variant_effect">
-                <param name="ref_genome_file" type="data" format="fasta" label="Dataset containing reference genomic sequence" help="fasta"/>
+                <param name="ref_genome_file" type="data" format="fasta" label="Dataset containing reference genomic sequence" help="fasta" />
                 <param name="blacklist_regions" type="select" label="blacklist regioins" help="A pre-loaded list of blacklisted intervals.Refer to `selene` for details.">
                     <option value="none" selected="true">None</option>
                     <option value="hg38">hg38</option>
                     <option value="hg19">hg19</option>
                 </param>
-                <param name="vcf_file" type="data" format="vcf" label="Dataset containing sequence variations" help="vcf"/>
-                <param name="seq_length" type="integer" value="1000" label="Encoding seqence length" help="A stretch of sequence surrounding the variation position on the reference genome."/>
-                <param name="output_reference" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Predict the reference sequence?" help="If False, predict on the variant sequence."/>
+                <param name="vcf_file" type="data" format="vcf" label="Dataset containing sequence variations" help="vcf" />
+                <param name="seq_length" type="integer" value="1000" label="Encoding seqence length" help="A stretch of sequence surrounding the variation position on the reference genome." />
+                <param name="output_reference" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Predict the reference sequence?" help="If False, predict on the variant sequence." />
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="tabular" name="outfile_predict"/>
+        <data format="tabular" name="outfile_predict" />
     </outputs>
     <tests>
         <test>
-            <param name="infile_estimator" value="best_estimator_.zip" ftype="zip"/>
-            <param name="method" value="predict"/>
-            <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
+            <param name="infile_estimator" value="best_estimator_.zip" ftype="zip" />
+            <param name="method" value="predict" />
+            <param name="infile1" value="regression_X.tabular" ftype="tabular" />
             <param name="header1" value="true" />
-            <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
-            <output name="outfile_predict" file="model_pred01.tabular"/>
+            <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
+            <output name="outfile_predict" file="model_pred01.tabular" />
         </test>
         <test>
-            <param name="infile_estimator" value="keras_model04" ftype="zip"/>
-            <param name="infile_weights" value="train_test_eval_weights02.h5" ftype="h5"/>
-            <param name="method" value="predict"/>
-            <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
+            <param name="infile_estimator" value="keras_model04" ftype="zip" />
+            <param name="infile_weights" value="train_test_eval_weights02.h5" ftype="h5" />
+            <param name="method" value="predict" />
+            <param name="infile1" value="regression_X.tabular" ftype="tabular" />
             <param name="header1" value="true" />
-            <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17"/>
-            <output name="outfile_predict" >
+            <param name="col1" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17" />
+            <output name="outfile_predict">
                 <assert_contents>
-                    <has_n_columns n="1"/>
-                    <has_text text="70.2"/>
-                    <has_text text="61.2"/>
-                    <has_text text="74.2"/>
-                    <has_text text="65.9"/>
-                    <has_text text="52.9"/>
+                    <has_n_columns n="1" />
+                    <has_text text="70.2" />
+                    <has_text text="61.2" />
+                    <has_text text="74.2" />
+                    <has_text text="65.9" />
+                    <has_text text="52.9" />
                 </assert_contents>
             </output>
         </test>
@@ -123,7 +123,7 @@
         ]]>
     </help>
     <expand macro="sklearn_citation">
-        <expand macro="keras_citation"/>
-        <expand macro="selene_citation"/>
+        <expand macro="keras_citation" />
+        <expand macro="selene_citation" />
     </expand>
 </tool>