Mercurial > repos > bgruening > sklearn_pairwise_metrics

diff pairwise_metrics.xml @ 35:dbbe397b64ad draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
author bgruening
date Tue, 13 Apr 2021 17:36:50 +0000
parents bc17040617c0
children 053e7f32d37e
line wrap: on
line diff
--- a/pairwise_metrics.xml	Thu Oct 01 20:11:05 2020 +0000
+++ b/pairwise_metrics.xml	Tue Apr 13 17:36:50 2021 +0000
@@ -1,10 +1,10 @@
-<tool id="sklearn_pairwise_metrics" name="Evaluate pairwise distances" version="@VERSION@">
+<tool id="sklearn_pairwise_metrics" name="Evaluate pairwise distances" version="@VERSION@" profile="20.05">
     <description>or compute affinity or kernel for sets of samples</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[
@@ -64,90 +64,90 @@
                 <option value="sparse">Sparse matrix (.mtx)</option>
             </param>
             <when value="tabular">
-                <expand macro="multiple_input" max_num="2" format="tabular"/>
+                <expand macro="multiple_input" max_num="2" format="tabular" />
                 <conditional name="metric_functions">
                     <expand macro="sparse_pairwise_metric_functions">
-                        <expand macro="pairwise_metric_functions"/>
+                        <expand macro="pairwise_metric_functions" />
                     </expand>
                     <when value="additive_chi2_kernel">
                     </when>
                     <when value="chi2_kernel">
                         <section name="options" title="Advanced Options" expanded="False">
-                            <expand macro="gamma" help_text="Floating point scaling parameter of the chi2 kernel. "/>
+                            <expand macro="gamma" help_text="Floating point scaling parameter of the chi2 kernel. " />
                         </section>
                     </when>
                     <when value="linear_kernel">
                     </when>
                     <when value="manhattan_distances">
                         <section name="options" title="Advanced Options" expanded="False">
-                            <param argument="sum_over_features" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Sum over features" help="If True, return the pairwise distance matrix, else return the componentwise L1 pairwise-distances. "/>
+                            <param argument="sum_over_features" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Sum over features" help="If True, return the pairwise distance matrix, else return the componentwise L1 pairwise-distances. " />
                         </section>
                     </when>
                     <when value="polynomial_kernel">
                         <section name="options" title="Advanced Options" expanded="False">
-                            <expand macro="gamma" default_value=""/>
-                            <expand macro="degree"/>
-                            <expand macro="coef0"/>
+                            <expand macro="gamma" default_value="" />
+                            <expand macro="degree" />
+                            <expand macro="coef0" />
                         </section>
                     </when>
                     <when value="rbf_kernel">
                         <section name="options" title="Advanced Options" expanded="False">
-                            <expand macro="gamma" default_value=""/>
+                            <expand macro="gamma" default_value="" />
                         </section>
                     </when>
                     <when value="laplacian_kernel">
                         <section name="options" title="Advanced Options" expanded="False">
-                            <expand macro="gamma" default_value=""/>
+                            <expand macro="gamma" default_value="" />
                         </section>
                     </when>
                     <when value="pairwise_kernels">
                         <section name="options" title="Advanced Options" expanded="False">
-                            <expand macro="pairwise_kernel_metrics"/>
+                            <expand macro="pairwise_kernel_metrics" />
                         </section>
                     </when>
                     <expand macro="sparse_pairwise_condition">
-                        <expand macro="distance_nonsparse_metrics"/>
+                        <expand macro="distance_nonsparse_metrics" />
                     </expand>
                     <expand macro="argmin_distance_condition">
-                        <expand macro="distance_nonsparse_metrics"/>
+                        <expand macro="distance_nonsparse_metrics" />
                     </expand>
                 </conditional>
             </when>
             <when value="sparse">
-                <expand macro="multiple_input" max_num="2"/>
+                <expand macro="multiple_input" max_num="2" />
                 <conditional name="metric_functions">
-                    <expand macro="sparse_pairwise_metric_functions"/>
-                    <expand macro="sparse_pairwise_condition"/>
-                    <expand macro="argmin_distance_condition"/>
+                    <expand macro="sparse_pairwise_metric_functions" />
+                    <expand macro="sparse_pairwise_condition" />
+                    <expand macro="argmin_distance_condition" />
                 </conditional>
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="tabular" name="outfile"/>
+        <data format="tabular" name="outfile" />
     </outputs>
     <tests>
         <test>
-            <param name="selected_input_type" value="tabular"/>
-            <param name="selected_metric_function" value="rbf_kernel"/>
-            <param name="input_files_0|input" value="test.tabular" ftype="tabular"/>
-            <param name="input_files_1|input" value="test2.tabular" ftype="tabular"/>
-            <param name="gamma" value="0.5"/>
+            <param name="selected_input_type" value="tabular" />
+            <param name="selected_metric_function" value="rbf_kernel" />
+            <param name="input_files_0|input" value="test.tabular" ftype="tabular" />
+            <param name="input_files_1|input" value="test2.tabular" ftype="tabular" />
+            <param name="gamma" value="0.5" />
             <output name="outfile" file="pw_metric01.tabular" compare="sim_size" />
         </test>
         <test>
-            <param name="selected_input_type" value="tabular"/>
-            <param name="selected_metric_function" value="pairwise_distances"/>
-            <param name="metric" value="manhattan"/>
-            <param name="input_files_0|input" value="test.tabular" ftype="tabular"/>
-            <output name="outfile" file="pw_metric02.tabular" lines_diff="4"/>
+            <param name="selected_input_type" value="tabular" />
+            <param name="selected_metric_function" value="pairwise_distances" />
+            <param name="metric" value="manhattan" />
+            <param name="input_files_0|input" value="test.tabular" ftype="tabular" />
+            <output name="outfile" file="pw_metric02.tabular" lines_diff="4" />
         </test>
         <test>
-            <param name="selected_input_type" value="sparse"/>
-            <param name="selected_metric_function" value="pairwise_distances"/>
-            <param name="metric" value="cosine"/>
-            <param name="input_files_0|input" value="sparse.mtx" ftype="txt"/>
-            <output name="outfile" file="pw_metric03.tabular"/>
+            <param name="selected_input_type" value="sparse" />
+            <param name="selected_metric_function" value="pairwise_distances" />
+            <param name="metric" value="cosine" />
+            <param name="input_files_0|input" value="sparse.mtx" ftype="txt" />
+            <output name="outfile" file="pw_metric03.tabular" />
         </test>
     </tests>
     <help>
@@ -160,5 +160,5 @@
 http://scikit-learn.org/stable/modules/metrics.html#metrics
         ]]>
     </help>
-    <expand macro="sklearn_citation"/>
+    <expand macro="sklearn_citation" />
 </tool>