diff numeric_clustering.xml @ 34:816b65d52c33 draft

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

--- a/numeric_clustering.xml	Thu Oct 01 20:40:11 2020 +0000
+++ b/numeric_clustering.xml	Tue Apr 13 18:05:02 2021 +0000
@@ -1,19 +1,19 @@
-<tool id="sklearn_numeric_clustering" name="Numeric Clustering" version="@VERSION@">
+<tool id="sklearn_numeric_clustering" name="Numeric Clustering" version="@VERSION@" profile="20.05">
     <description></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[
     python "$cluster_script" '$inputs'
 ]]>
     </command>
     <configfiles>
-        <inputs name="inputs"/>
+        <inputs name="inputs" />
         <configfile name="cluster_script">
-<![CDATA[
+            <![CDATA[
 import sys
 import json
 import numpy as np
@@ -89,14 +89,14 @@
                 <option value="sparse">Sparse Vector Representation (mtx)</option>
             </param>
             <when value="sparse">
-                <param name="infile" type="data" format="txt" label="Sparse vector (scipy.sparse.csr_matrix) file:" help="The following clustering algorithms support sparse matrix operations: ''Birch'', ''DBSCAN'', ''KMeans'', ''Mini BatchK Means'', and ''Spectral Clustering''. If your data is in tabular format, please use other clustering algorithms."/>
-                <expand macro="clustering_algorithms_options"/>
+                <param name="infile" type="data" format="txt" label="Sparse vector (scipy.sparse.csr_matrix) file:" help="The following clustering algorithms support sparse matrix operations: ''Birch'', ''DBSCAN'', ''KMeans'', ''Mini BatchK Means'', and ''Spectral Clustering''. If your data is in tabular format, please use other clustering algorithms." />
+                <expand macro="clustering_algorithms_options" />
             </when>
             <when value="tabular">
-                <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
+                <param name="infile" type="data" format="tabular" label="Data file with numeric values" />
                 <param name="header" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="True" label="Does the dataset contain header:" />
                 <conditional name="column_selector_options">
-                    <expand macro="samples_column_selector_options" col_name="col" multiple="true" infile="infile"/>
+                    <expand macro="samples_column_selector_options" col_name="col" multiple="true" infile="infile" />
                 </conditional>
                 <!--expand macro="clustering_algorithms_options"-->
                 <conditional name="algorithm_options">
@@ -111,26 +111,26 @@
                         <option value="Birch">Birch</option>
                     </param>
                     <when value="KMeans">
-                        <expand macro="kmeans_advanced_options"/>
+                        <expand macro="kmeans_advanced_options" />
                     </when>
                     <when value="DBSCAN">
-                        <expand macro="dbscan_advanced_options"/>
+                        <expand macro="dbscan_advanced_options" />
                     </when>
                     <when value="Birch">
-                        <expand macro="birch_advanced_options"/>
+                        <expand macro="birch_advanced_options" />
                     </when>
                     <when value="SpectralClustering">
-                        <expand macro="spectral_clustering_advanced_options"/>
+                        <expand macro="spectral_clustering_advanced_options" />
                     </when>
                     <when value="MiniBatchKMeans">
-                        <expand macro="minibatch_kmeans_advanced_options"/>
+                        <expand macro="minibatch_kmeans_advanced_options" />
                     </when>
                     <when value="AffinityPropagation">
                         <section name="options" title="Advanced Options" expanded="False">
-                            <param argument="damping" type="float" optional="true" value="0.5" label="Damping factor" help="Damping factor between 0.5 and 1."/>
-                            <expand macro="max_iter" default_value="200"/>
-                            <param argument="convergence_iter" type="integer" optional="true" value="15" label="Number of iterations at each convergence step" help="Number of iterations with no change in the number of estimated clusters that stops the convergence."/>
-                            <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Copy" help="If False, the affinity matrix is modified inplace by the algorithm, for memory efficiency."/>
+                            <param argument="damping" type="float" optional="true" value="0.5" label="Damping factor" help="Damping factor between 0.5 and 1." />
+                            <expand macro="max_iter" default_value="200" />
+                            <param argument="convergence_iter" type="integer" optional="true" value="15" label="Number of iterations at each convergence step" help="Number of iterations with no change in the number of estimated clusters that stops the convergence." />
+                            <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Copy" help="If False, the affinity matrix is modified inplace by the algorithm, for memory efficiency." />
                             <!--param argument="preference"/-->
                             <param argument="affinity" type="select" label="Affinity" help="Affinity to use; euclidean uses the negative squared euclidean distance between points.">
                                 <option value="euclidean">Euclidean</option>
@@ -140,11 +140,11 @@
                     </when>
                     <when value="MeanShift">
                         <section name="options" title="Advanced Options" expanded="False">
-                            <param argument="bandwidth" type="float" optional="true" value="" label="Kernel bandwidth" help="Bandwidth used in the RBF kernel. If not given, it will be computed using a heuristic based on the median of all pairwise distances."/>
+                            <param argument="bandwidth" type="float" optional="true" value="" label="Kernel bandwidth" help="Bandwidth used in the RBF kernel. If not given, it will be computed using a heuristic based on the median of all pairwise distances." />
                             <!--param argument="seeds"/-->
-                            <param argument="bin_seeding" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Discretize initial kernel locations" help="If true, initial kernel locations are the bins grid whose coarseness corresponds to the bandwidth, speeding up the algorithm."/>
-                            <param argument="min_bin_freq" type="integer" optional="true" value="1" label="Minimum number of seeds per bin" help="To speed up the algorithm, accept only those bins with at least min_bin_freq points as seeds."/>
-                            <param argument="cluster_all" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Cluster all" help="If true, all points (including orphans) are clustered. If false, orphans are given cluster label -1."/>
+                            <param argument="bin_seeding" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Discretize initial kernel locations" help="If true, initial kernel locations are the bins grid whose coarseness corresponds to the bandwidth, speeding up the algorithm." />
+                            <param argument="min_bin_freq" type="integer" optional="true" value="1" label="Minimum number of seeds per bin" help="To speed up the algorithm, accept only those bins with at least min_bin_freq points as seeds." />
+                            <param argument="cluster_all" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Cluster all" help="If true, all points (including orphans) are clustered. If false, orphans are given cluster label -1." />
                         </section>
                     </when>
                     <when value="AgglomerativeClustering">
@@ -176,212 +176,212 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="tabular" name="outfile"/>
+        <data format="tabular" name="outfile" />
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_input_type" value="tabular"/>
-            <param name="selected_algorithm" value="KMeans"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_input_type" value="tabular" />
+            <param name="selected_algorithm" value="KMeans" />
             <param name="col" value="2,3,4" />
             <param name="n_clusters" value="4" />
             <param name="init" value="k-means++" />
-            <param name="random_state" value="100"/>
-            <output name="outfile" file="cluster_result01.txt"/>
+            <param name="random_state" value="100" />
+            <output name="outfile" file="cluster_result01.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="KMeans"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="KMeans" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
             <param name="n_clusters" value="4" />
             <param name="init" value="random" />
-            <param name="random_state" value="100"/>
-            <output name="outfile" file="cluster_result02.txt"/>
+            <param name="random_state" value="100" />
+            <output name="outfile" file="cluster_result02.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="DBSCAN"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="DBSCAN" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="algorithm" value="kd_tree"/>
-            <param name="leaf_size" value="10"/>
-            <param name="eps" value="1.0"/>
-            <output name="outfile" file="cluster_result03.txt"/>
+            <param name="algorithm" value="kd_tree" />
+            <param name="leaf_size" value="10" />
+            <param name="eps" value="1.0" />
+            <output name="outfile" file="cluster_result03.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="Birch"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="Birch" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="n_clusters" value="4"/>
-            <param name="threshold" value="0.008"/>
-            <output name="outfile" file="cluster_result04.txt"/>
+            <param name="n_clusters" value="4" />
+            <param name="threshold" value="0.008" />
+            <output name="outfile" file="cluster_result04.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="Birch"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="Birch" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="branching_factor" value="20"/>
-            <output name="outfile" file="cluster_result05.txt"/>
+            <param name="branching_factor" value="20" />
+            <output name="outfile" file="cluster_result05.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="AffinityPropagation"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="AffinityPropagation" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="affinity" value="euclidean"/>
-            <param name="copy" value="false"/>
-            <output name="outfile" file="cluster_result06.txt"/>
+            <param name="affinity" value="euclidean" />
+            <param name="copy" value="false" />
+            <output name="outfile" file="cluster_result06.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="AffinityPropagation"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="AffinityPropagation" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="damping" value="0.8"/>
-            <output name="outfile" file="cluster_result07.txt"/>
+            <param name="damping" value="0.8" />
+            <output name="outfile" file="cluster_result07.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="MeanShift"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="MeanShift" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="min_bin_freq" value="3"/>
-            <output name="outfile" file="cluster_result08.txt"/>
+            <param name="min_bin_freq" value="3" />
+            <output name="outfile" file="cluster_result08.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="MeanShift"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="MeanShift" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="cluster_all" value="False"/>
-            <output name="outfile" file="cluster_result09.txt"/>
+            <param name="cluster_all" value="False" />
+            <output name="outfile" file="cluster_result09.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="AgglomerativeClustering"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="AgglomerativeClustering" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="affinity" value="euclidean"/>
-            <param name="linkage" value="average"/>
-            <param name="n_clusters" value="4"/>
-            <output name="outfile" file="cluster_result10.txt"/>
+            <param name="affinity" value="euclidean" />
+            <param name="linkage" value="average" />
+            <param name="n_clusters" value="4" />
+            <output name="outfile" file="cluster_result10.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="AgglomerativeClustering"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="AgglomerativeClustering" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="linkage" value="complete"/>
-            <param name="n_clusters" value="4"/>
-            <output name="outfile" file="cluster_result11.txt"/>
+            <param name="linkage" value="complete" />
+            <param name="n_clusters" value="4" />
+            <output name="outfile" file="cluster_result11.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="SpectralClustering"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="SpectralClustering" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="eigen_solver" value="arpack"/>
-            <param name="n_neighbors" value="12"/>
-            <param name="n_clusters" value="4"/>
-            <param name="assign_labels" value="discretize"/>
-            <param name="random_state" value="100"/>
+            <param name="eigen_solver" value="arpack" />
+            <param name="n_neighbors" value="12" />
+            <param name="n_clusters" value="4" />
+            <param name="assign_labels" value="discretize" />
+            <param name="random_state" value="100" />
             <output name="outfile" file="cluster_result12.txt" compare="sim_size" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="SpectralClustering"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="SpectralClustering" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="assign_labels" value="discretize"/>
-            <param name="random_state" value="100"/>
-            <param name="degree" value="2"/>
+            <param name="assign_labels" value="discretize" />
+            <param name="random_state" value="100" />
+            <param name="degree" value="2" />
             <output name="outfile" file="cluster_result13.txt" compare="sim_size" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="MiniBatchKMeans"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="MiniBatchKMeans" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
-            <param name="tol" value="0.5"/>
-            <param name="random_state" value="100"/>
-            <output name="outfile" file="cluster_result14.txt"/>
+            <param name="tol" value="0.5" />
+            <param name="random_state" value="100" />
+            <output name="outfile" file="cluster_result14.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="MiniBatchKMeans"/>
-            <param name="selected_input_type" value="tabular"/>
-            <param name="n_init" value="5"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="MiniBatchKMeans" />
+            <param name="selected_input_type" value="tabular" />
+            <param name="n_init" value="5" />
             <param name="col" value="2,3,4" />
-            <param name="batch_size" value="10"/>
-            <param name="n_clusters" value="4"/>
-            <param name="random_state" value="100"/>
-            <param name="reassignment_ratio" value="1.0"/>
-            <output name="outfile" file="cluster_result15.txt"/>
+            <param name="batch_size" value="10" />
+            <param name="n_clusters" value="4" />
+            <param name="random_state" value="100" />
+            <param name="reassignment_ratio" value="1.0" />
+            <output name="outfile" file="cluster_result15.txt" />
         </test>
         <test>
-            <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
-            <param name="selected_algorithm" value="KMeans"/>
-            <param name="selected_input_type" value="tabular"/>
+            <param name="infile" value="numeric_values.tabular" ftype="tabular" />
+            <param name="selected_algorithm" value="KMeans" />
+            <param name="selected_input_type" value="tabular" />
             <param name="col" value="1" />
             <param name="n_clusters" value="4" />
-            <param name="random_state" value="100"/>
-            <output name="outfile" file="cluster_result16.txt"/>
+            <param name="random_state" value="100" />
+            <output name="outfile" file="cluster_result16.txt" />
         </test>
         <test>
-            <param name="infile" value="sparse.mtx" ftype="txt"/>
-            <param name="selected_input_type" value="sparse"/>
-            <param name="selected_algorithm" value="KMeans"/>
+            <param name="infile" value="sparse.mtx" ftype="txt" />
+            <param name="selected_input_type" value="sparse" />
+            <param name="selected_algorithm" value="KMeans" />
             <param name="n_clusters" value="2" />
             <param name="init" value="k-means++" />
-            <param name="random_state" value="100"/>
-            <output name="outfile" file="cluster_result17.txt"/>
+            <param name="random_state" value="100" />
+            <output name="outfile" file="cluster_result17.txt" />
         </test>
         <test>
-            <param name="infile" value="sparse.mtx" ftype="txt"/>
-            <param name="selected_algorithm" value="DBSCAN"/>
-            <param name="selected_input_type" value="sparse"/>
-            <param name="algorithm" value="kd_tree"/>
-            <param name="leaf_size" value="10"/>
-            <param name="eps" value="1.0"/>
-            <output name="outfile" file="cluster_result18.txt"/>
+            <param name="infile" value="sparse.mtx" ftype="txt" />
+            <param name="selected_algorithm" value="DBSCAN" />
+            <param name="selected_input_type" value="sparse" />
+            <param name="algorithm" value="kd_tree" />
+            <param name="leaf_size" value="10" />
+            <param name="eps" value="1.0" />
+            <output name="outfile" file="cluster_result18.txt" />
         </test>
         <test>
-            <param name="infile" value="sparse.mtx" ftype="txt"/>
-            <param name="selected_algorithm" value="Birch"/>
-            <param name="selected_input_type" value="sparse"/>
-            <param name="n_clusters" value="2"/>
-            <param name="threshold" value="0.008"/>
-            <output name="outfile" file="cluster_result19.txt"/>
+            <param name="infile" value="sparse.mtx" ftype="txt" />
+            <param name="selected_algorithm" value="Birch" />
+            <param name="selected_input_type" value="sparse" />
+            <param name="n_clusters" value="2" />
+            <param name="threshold" value="0.008" />
+            <output name="outfile" file="cluster_result19.txt" />
         </test>
         <test>
-            <param name="infile" value="sparse.mtx" ftype="txt"/>
-            <param name="selected_algorithm" value="MiniBatchKMeans"/>
-            <param name="selected_input_type" value="sparse"/>
-            <param name="n_init" value="5"/>
-            <param name="batch_size" value="10"/>
-            <param name="n_clusters" value="2"/>
-            <param name="random_state" value="100"/>
-            <param name="reassignment_ratio" value="1.0"/>
-            <output name="outfile" file="cluster_result20.txt"/>
+            <param name="infile" value="sparse.mtx" ftype="txt" />
+            <param name="selected_algorithm" value="MiniBatchKMeans" />
+            <param name="selected_input_type" value="sparse" />
+            <param name="n_init" value="5" />
+            <param name="batch_size" value="10" />
+            <param name="n_clusters" value="2" />
+            <param name="random_state" value="100" />
+            <param name="reassignment_ratio" value="1.0" />
+            <output name="outfile" file="cluster_result20.txt" />
         </test>
         <test>
-            <param name="infile" value="sparse.mtx" ftype="txt"/>
-            <param name="selected_algorithm" value="SpectralClustering"/>
-            <param name="selected_input_type" value="sparse"/>
-            <param name="assign_labels" value="discretize"/>
-            <param name="n_clusters" value="2"/>
-            <param name="random_state" value="100"/>
-            <param name="degree" value="2"/>
-            <output name="outfile" file="cluster_result21.txt"/>
+            <param name="infile" value="sparse.mtx" ftype="txt" />
+            <param name="selected_algorithm" value="SpectralClustering" />
+            <param name="selected_input_type" value="sparse" />
+            <param name="assign_labels" value="discretize" />
+            <param name="n_clusters" value="2" />
+            <param name="random_state" value="100" />
+            <param name="degree" value="2" />
+            <output name="outfile" file="cluster_result21.txt" />
         </test>
     </tests>
     <help><![CDATA[
 **What it does**
 This tool offers different clustering algorithms which are provided by
 scikit-learn to find similarities among samples and cluster the samples based on these similarities.
-    ]]></help>
-    <expand macro="sklearn_citation"/>
+    ]]>    </help>
+    <expand macro="sklearn_citation" />
 </tool>