Mercurial > repos > bgruening > sklearn_numeric_clustering

diff numeric_clustering.xml @ 40:06d772036a62 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 13:11:48 +0000
parents 816b65d52c33
children
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--- a/numeric_clustering.xml	Thu Aug 11 08:51:18 2022 +0000
+++ b/numeric_clustering.xml	Wed Aug 09 13:11:48 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="sklearn_numeric_clustering" name="Numeric Clustering" version="@VERSION@" profile="20.05">
+<tool id="sklearn_numeric_clustering" name="Numeric Clustering" version="@VERSION@" profile="@PROFILE@">
     <description></description>
     <macros>
         <import>main_macros.xml</import>
@@ -42,10 +42,12 @@
 if 'n_jobs' in cluster_object.get_params():
     cluster_object.set_params( n_jobs=N_JOBS )
 
+header = None
 #if $input_types.selected_input_type == "sparse":
 data_matrix = mmread("$infile")
 #else:
-data = pandas.read_csv("$infile", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None)
+data = pandas.read_csv("$infile", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None)
+
 header = 'infer' if params["input_types"]["header"] else None
 column_option = params["input_types"]["column_selector_options"]["selected_column_selector_option"]
 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
@@ -183,6 +185,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_input_type" value="tabular" />
             <param name="selected_algorithm" value="KMeans" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="n_clusters" value="4" />
             <param name="init" value="k-means++" />
@@ -193,6 +196,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="KMeans" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="n_clusters" value="4" />
             <param name="init" value="random" />
@@ -203,6 +207,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="DBSCAN" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="algorithm" value="kd_tree" />
             <param name="leaf_size" value="10" />
@@ -213,6 +218,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="Birch" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="n_clusters" value="4" />
             <param name="threshold" value="0.008" />
@@ -222,6 +228,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="Birch" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="branching_factor" value="20" />
             <output name="outfile" file="cluster_result05.txt" />
@@ -230,6 +237,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="AffinityPropagation" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="affinity" value="euclidean" />
             <param name="copy" value="false" />
@@ -239,6 +247,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="AffinityPropagation" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="damping" value="0.8" />
             <output name="outfile" file="cluster_result07.txt" />
@@ -247,6 +256,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="MeanShift" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="min_bin_freq" value="3" />
             <output name="outfile" file="cluster_result08.txt" />
@@ -255,6 +265,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="MeanShift" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="cluster_all" value="False" />
             <output name="outfile" file="cluster_result09.txt" />
@@ -263,6 +274,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="AgglomerativeClustering" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="affinity" value="euclidean" />
             <param name="linkage" value="average" />
@@ -273,6 +285,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="AgglomerativeClustering" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="linkage" value="complete" />
             <param name="n_clusters" value="4" />
@@ -283,6 +296,7 @@
             <param name="selected_algorithm" value="SpectralClustering" />
             <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
+            <param name="header" value="false" />
             <param name="eigen_solver" value="arpack" />
             <param name="n_neighbors" value="12" />
             <param name="n_clusters" value="4" />
@@ -295,6 +309,7 @@
             <param name="selected_algorithm" value="SpectralClustering" />
             <param name="selected_input_type" value="tabular" />
             <param name="col" value="2,3,4" />
+            <param name="header" value="false" />
             <param name="assign_labels" value="discretize" />
             <param name="random_state" value="100" />
             <param name="degree" value="2" />
@@ -304,6 +319,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="MiniBatchKMeans" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="2,3,4" />
             <param name="tol" value="0.5" />
             <param name="random_state" value="100" />
@@ -313,6 +329,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="MiniBatchKMeans" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="n_init" value="5" />
             <param name="col" value="2,3,4" />
             <param name="batch_size" value="10" />
@@ -325,6 +342,7 @@
             <param name="infile" value="numeric_values.tabular" ftype="tabular" />
             <param name="selected_algorithm" value="KMeans" />
             <param name="selected_input_type" value="tabular" />
+            <param name="header" value="false" />
             <param name="col" value="1" />
             <param name="n_clusters" value="4" />
             <param name="random_state" value="100" />