diff clf_metrics.xml @ 35:3c5034b0d775 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 208a8d348e7c7a182cfbe1b6f17868146428a7e2"

--- a/clf_metrics.xml	Wed Mar 11 17:13:28 2020 +0000
+++ b/clf_metrics.xml	Tue Apr 13 21:08:12 2021 +0000
@@ -1,10 +1,10 @@
-<tool id="sklearn_clf_metrics" name="Calculate metrics" version="@VERSION@">
+<tool id="sklearn_clf_metrics" name="Calculate metrics" version="@VERSION@" profile="20.05">
     <description>for classification performance</description>
     <macros>
         <import>main_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[
@@ -94,163 +94,160 @@
                 <option value="roc_auc_score">Area Under the Curve (AUC) from prediction scores</option>
             </param>
             <when value="accuracy_score">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <!--sample_weight-->
-                    <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
-                        label="Normalize" help="If false, returns the number of correctly classified samples. Otherwise, returns the fraction of correctly classified samples. "/>
+                    <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the number of correctly classified samples. Otherwise, returns the fraction of correctly classified samples. " />
                 </section>
             </when>
             <when value="classification_report">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <!--labels-->
                     <!--target_names-->
                     <!--sample_weight-->
-                    <param argument="digits" type="integer" value="2" label="Number of digits for formatting output floating point values" help=""/>
+                    <param argument="digits" type="integer" value="2" label="Number of digits for formatting output floating point values" help="" />
                 </section>
             </when>
             <when value="f1_score">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <!--labels-->
                     <!--sample_weight-->
-                    <expand macro="pos_label" default_value="1"/>
+                    <expand macro="pos_label" default_value="1" />
                     <expand macro="average">
                         <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
                     </expand>
                 </section>
             </when>
             <when value="fbeta_score">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
-                    <expand macro="beta"/>
+                    <expand macro="beta" />
                     <!--labels-->
                     <!--sample_weight-->
-                    <expand macro="pos_label" default_value="1"/>
+                    <expand macro="pos_label" default_value="1" />
                     <expand macro="average">
                         <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
                     </expand>
                 </section>
             </when>
             <when value="hamming_loss">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <!--section name="options" title="Advanced Options" expanded="False">
                     <!- -classes- ->
                 </section-->
             </when>
             <when value="jaccard_similarity_score">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
-                    <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the sum of the Jaccard similarity coefficient over the sample set. Otherwise, returns the average of Jaccard similarity coefficient. "/>
+                    <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the sum of the Jaccard similarity coefficient over the sample set. Otherwise, returns the average of Jaccard similarity coefficient. " />
                 </section>
             </when>
             <when value="precision_recall_fscore_support">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
-                    <expand macro="beta"/>
+                    <expand macro="beta" />
                     <!--labels-->
                     <!--sample_weight-->
                     <!--warn_for-->
-                    <expand macro="pos_label" default_value="1"/>
+                    <expand macro="pos_label" default_value="1" />
                     <expand macro="average">
                         <option value="binary" selected="true">Only report results for the class specified by pos_label. Applicable only on binary classification. (binary)</option>
                     </expand>
                 </section>
             </when>
             <when value="precision_score">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <!--labels-->
                     <!--sample_weight-->
-                    <expand macro="pos_label" default_value="1"/>
+                    <expand macro="pos_label" default_value="1" />
                     <expand macro="average">
                         <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
                     </expand>
                 </section>
             </when>
             <when value="recall_score">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <!--labels-->
                     <!--sample_weight-->
-                    <expand macro="pos_label" default_value="1"/>
+                    <expand macro="pos_label" default_value="1" />
                     <expand macro="average">
                         <option value="binary" selected="true">Only report results for the class specified by pos_label. This is applicable only if targets (y_{true,pred}) are binary. (binary)</option>
                     </expand>
                 </section>
             </when>
             <when value="zero_one_loss">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <!--sample_weight-->
-                    <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the number of misclassifications. Otherwise, returns the fraction of misclassifications. "/>
+                    <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If false, returns the number of misclassifications. Otherwise, returns the fraction of misclassifications. " />
                 </section>
             </when>
             <when value="auc">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
-                     <param argument="reorder" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Assume an ascending curve in the case of ties" help="If the curve is non-ascending, the result will be wrong. "/>
+                    <param argument="reorder" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Assume an ascending curve in the case of ties" help="If the curve is non-ascending, the result will be wrong. " />
                 </section>
             </when>
             <when value="brier_score_loss">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <!--weights-->
-                    <expand macro="pos_label"/>
+                    <expand macro="pos_label" />
                 </section>
             </when>
             <when value="matthews_corrcoef">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <!--section name="options" title="Advanced Options" expanded="False">
                 </section-->
             </when>
             <when value="confusion_matrix">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <!--section name="options" title="Advanced Options" expanded="False">
                     <!- -labels- ->
                 </section-->
             </when>
             <when value="precision_recall_curve">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
-                    <expand macro="pos_label"/>
+                    <expand macro="pos_label" />
                     <!--sample_weight-->
                 </section>
             </when>
             <when value="roc_curve">
-                <expand macro="clf_inputs"/>
+                <expand macro="clf_inputs" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <!--sample_weight-->
-                    <expand macro="pos_label"/>
-                    <param argument="drop_intermediate" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label=" Drop suboptimal thresholds" help="This is useful in order to create lighter ROC curves. "/>
+                    <expand macro="pos_label" />
+                    <param argument="drop_intermediate" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label=" Drop suboptimal thresholds" help="This is useful in order to create lighter ROC curves. " />
                 </section>
             </when>
             <when value="hinge_loss">
-                <expand macro="clf_inputs" multiple="true"/>
+                <expand macro="clf_inputs" multiple="true" />
                 <!--section name="options" title="Advanced Options" expanded="False">
                     <!- -labels- ->
                     <!- -sample_weight- ->
                 </section-->
             </when>
             <when value="log_loss">
-                <expand macro="clf_inputs" multiple="true"/>
+                <expand macro="clf_inputs" multiple="true" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <!--sample_weight-->
-                    <param argument="eps" type="float" value="1e-15" label="Clipping factor"
-                        help="Log loss is undefined for p=0 or p=1, so probabilities are     clipped to max(eps, min(1 - eps, p)). "/>
-                    <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
-                        label="Normalize" help="If true, returns the mean loss per sample. Otherwise, returns the sum of the per-sample losses. "/>
+                    <param argument="eps" type="float" value="1e-15" label="Clipping factor" help="Log loss is undefined for p=0 or p=1, so probabilities are     clipped to max(eps, min(1 - eps, p)). " />
+                    <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Normalize" help="If true, returns the mean loss per sample. Otherwise, returns the sum of the per-sample losses. " />
                 </section>
             </when>
             <when value="average_precision_score">
-                <expand macro="clf_inputs" multiple1="true" multiple="true"/>
+                <expand macro="clf_inputs" multiple1="true" multiple="true" />
                 <!-- section name="options" title="Advanced Options" expanded="False">
                     <!- -average='macro', sample_weight=None- ->
                 </section-->
             </when>
             <when value="roc_auc_score">
-                <expand macro="clf_inputs" multiple1="true" multiple="true"/>
+                <expand macro="clf_inputs" multiple1="true" multiple="true" />
                 <section name="options" title="Advanced Options" expanded="False">
                     <expand macro="average">
                         <option value="macro" selected="true">Calculate metrics for each label, and find their unweighted mean. (macro)</option>
@@ -260,174 +257,174 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="txt" name="outfile"/>
+        <data format="txt" name="outfile" />
     </outputs>
     <tests>
         <test>
-            <param name="selected_metric" value="accuracy_score"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <output name="outfile" file="accuracy_score.txt"/>
+            <param name="selected_metric" value="accuracy_score" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <output name="outfile" file="accuracy_score.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="classification_report"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <output name="outfile" file="classification_report.txt"/>
+            <param name="selected_metric" value="classification_report" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <output name="outfile" file="classification_report.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="f1_score"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <param name="average" value="micro"/>
-            <output name="outfile" file="f1_score.txt"/>
+            <param name="selected_metric" value="f1_score" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <param name="average" value="micro" />
+            <output name="outfile" file="f1_score.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="fbeta_score"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <param name="average" value="micro"/>
-            <output name="outfile" file="fbeta_score.txt"/>
+            <param name="selected_metric" value="fbeta_score" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <param name="average" value="micro" />
+            <output name="outfile" file="fbeta_score.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="hamming_loss"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <output name="outfile" file="hamming_loss.txt"/>
+            <param name="selected_metric" value="hamming_loss" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <output name="outfile" file="hamming_loss.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="jaccard_similarity_score"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <output name="outfile" file="jaccard_similarity_score.txt"/>
+            <param name="selected_metric" value="jaccard_similarity_score" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <output name="outfile" file="jaccard_similarity_score.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="precision_recall_fscore_support"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <param name="average" value="micro"/>
-            <output name="outfile" file="precision_recall_fscore_support.txt"/>
+            <param name="selected_metric" value="precision_recall_fscore_support" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <param name="average" value="micro" />
+            <output name="outfile" file="precision_recall_fscore_support.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="precision_score"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <param name="average" value="micro"/>
-            <output name="outfile" file="precision_score.txt"/>
+            <param name="selected_metric" value="precision_score" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <param name="average" value="micro" />
+            <output name="outfile" file="precision_score.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="recall_score"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <param name="average" value="micro"/>
-            <output name="outfile" file="recall_score.txt"/>
+            <param name="selected_metric" value="recall_score" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <param name="average" value="micro" />
+            <output name="outfile" file="recall_score.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="zero_one_loss"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <output name="outfile" file="zero_one_loss.txt"/>
+            <param name="selected_metric" value="zero_one_loss" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <output name="outfile" file="zero_one_loss.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="auc"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <param name="reorder" value="true"/>
-            <output name="outfile" file="auc.txt"/>
+            <param name="selected_metric" value="auc" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <param name="reorder" value="true" />
+            <output name="outfile" file="auc.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="brier_score_loss"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="6"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="4"/>
-            <output name="outfile" file="brier_score_loss.txt"/>
+            <param name="selected_metric" value="brier_score_loss" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="6" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="4" />
+            <output name="outfile" file="brier_score_loss.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="matthews_corrcoef"/>
-            <param name="infile1" value="y.tabular"/>
-            <param name="col1" value="6"/>
-            <param name="infile2" value="y.tabular"/>
-            <param name="col2" value="7"/>
-            <output name="outfile" file="matthews_corrcoef.txt"/>
+            <param name="selected_metric" value="matthews_corrcoef" />
+            <param name="infile1" value="y.tabular" />
+            <param name="col1" value="6" />
+            <param name="infile2" value="y.tabular" />
+            <param name="col2" value="7" />
+            <output name="outfile" file="matthews_corrcoef.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="confusion_matrix"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="2"/>
-            <output name="outfile" file="confusion_matrix.txt"/>
+            <param name="selected_metric" value="confusion_matrix" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="2" />
+            <output name="outfile" file="confusion_matrix.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="precision_recall_curve"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="6"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="7"/>
-            <output name="outfile" file="precision_recall_curve.txt"/>
+            <param name="selected_metric" value="precision_recall_curve" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="6" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="7" />
+            <output name="outfile" file="precision_recall_curve.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="roc_curve"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="6"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="7"/>
-            <output name="outfile" file="roc_curve.txt"/>
+            <param name="selected_metric" value="roc_curve" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="6" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="7" />
+            <output name="outfile" file="roc_curve.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="hinge_loss"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="1"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="8,9,10"/>
-            <output name="outfile" file="hinge_loss.txt"/>
+            <param name="selected_metric" value="hinge_loss" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="1" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="8,9,10" />
+            <output name="outfile" file="hinge_loss.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="log_loss"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="2"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="3,4,5"/>
-            <output name="outfile" file="log_loss.txt"/>
+            <param name="selected_metric" value="log_loss" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="2" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="3,4,5" />
+            <output name="outfile" file="log_loss.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="average_precision_score"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="6"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="7"/>
-            <output name="outfile" file="average_precision_score.txt"/>
+            <param name="selected_metric" value="average_precision_score" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="6" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="7" />
+            <output name="outfile" file="average_precision_score.txt" />
         </test>
         <test>
-            <param name="selected_metric" value="roc_auc_score"/>
-            <param name="infile1" value="y.tabular" ftype="tabular"/>
-            <param name="col1" value="6"/>
-            <param name="infile2" value="y.tabular" ftype="tabular"/>
-            <param name="col2" value="7"/>
-            <output name="outfile" file="roc_auc_score.txt"/>
+            <param name="selected_metric" value="roc_auc_score" />
+            <param name="infile1" value="y.tabular" ftype="tabular" />
+            <param name="col1" value="6" />
+            <param name="infile2" value="y.tabular" ftype="tabular" />
+            <param name="col2" value="7" />
+            <output name="outfile" file="roc_auc_score.txt" />
         </test>
     </tests>
     <help>
@@ -440,5 +437,5 @@
 .. _`Scikit-learn classification metrics`: http://scikit-learn.org/stable/modules/model_evaluation.html#classification-metrics
         ]]>
     </help>
-    <expand macro="sklearn_citation"/>
+    <expand macro="sklearn_citation" />
 </tool>