diff pca.xml @ 1:132805688fa3 draft

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

--- a/pca.xml	Fri Oct 02 08:45:21 2020 +0000
+++ b/pca.xml	Tue Apr 13 18:49:35 2021 +0000
@@ -1,11 +1,11 @@
-<tool id="sklearn_pca" name="Principal component analysis" version="@VERSION@+galaxy@GALAXY_VERSION@">
+<tool id="sklearn_pca" name="Principal component analysis" version="@VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
     <description>with scikit-learn</description>
     <macros>
         <import>main_macros.xml</import>
         <token name="@GALAXY_VERSION@">0</token>
     </macros>
-    <expand macro="python_requirements"/>
-    <expand macro="macro_stdio"/>
+    <expand macro="python_requirements" />
+    <expand macro="macro_stdio" />
     <version_command>echo "@VERSION@"</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
@@ -61,10 +61,10 @@
         ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="tabular" label="Input file"/>
-        <param name="header" type="boolean" label="Exclude Header" truevalue="--header" falsevalue="" help="If present, exclude the header row from the dataset"/>
+        <param name="infile" type="data" format="tabular" label="Input file" />
+        <param name="header" type="boolean" label="Exclude Header" truevalue="--header" falsevalue="" help="If present, exclude the header row from the dataset" />
         <conditional name="column_selector_options">
-            <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile"/>
+            <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile" />
         </conditional>
         <conditional name="select_pca_type">
             <param name="select_pca_opts" type="select" label="Select PCA Type" help="Choose which flavour of PCA to use">
@@ -73,8 +73,8 @@
                 <option value="kernel">Kernel PCA</option>
             </param>
             <when value="classical">
-                <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept"/>
-                <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue="" help="Setting this option will reduce the redundancy and correlations between the features"/>
+                <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept" />
+                <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue="" help="Setting this option will reduce the redundancy and correlations between the features" />
                 <conditional name="select_solver_type">
                     <param name="svd_solver_opts" type="select" label="SVD Solver" help="Method to perform the singular value decomposition">
                         <option value="auto" selected="true">auto</option>
@@ -83,20 +83,20 @@
                         <option value="randomized">randomized</option>
                     </param>
                     <when value="arpack">
-                        <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack"/>
+                        <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack" />
                     </when>
-                    <when value="auto"/>
-                    <when value="full"/>
-                    <when value="randomized"/>
+                    <when value="auto" />
+                    <when value="full" />
+                    <when value="randomized" />
                 </conditional>
             </when>
             <when value="incremental">
-                <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept"/>
-                <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue=""/>
-                <param name="batch_size" type="integer" optional="true" label="Batch Size" help="The number of samples to use for each batch"/>
+                <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept" />
+                <param name="whiten" type="boolean" label="Whiten Components" truevalue="--whiten" falsevalue="" />
+                <param name="batch_size" type="integer" optional="true" label="Batch Size" help="The number of samples to use for each batch" />
             </when>
             <when value="kernel">
-                <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept"/>
+                <param name="number" type="integer" optional="true" label="Number of components" help="Number of components to keep. If not set, all components are kept" />
                 <conditional name="select_kernel_opts">
                     <param name="kernel_opts" type="select" label="Kernel Type">
                         <option value="linear" selected="true">linear</option>
@@ -107,20 +107,20 @@
                         <option value="precomputed">precomputed</option>
                     </param>
                     <when value="poly">
-                        <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/>
-                        <param name="degree" type="integer" value="3" label="Degree of the polynomial" help="Degree for poly kernels. Ignored by other kernels"/>
-                        <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels"/>
+                        <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels" />
+                        <param name="degree" type="integer" value="3" label="Degree of the polynomial" help="Degree for poly kernels. Ignored by other kernels" />
+                        <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels" />
                     </when>
                     <when value="sigmoid">
-                        <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/>
-                        <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels"/>
+                        <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels" />
+                        <param name="coef0" type="float" value="1.0" label="Coef0" help="Independent term in poly and sigmoid kernels. Ignored by other kernels" />
                     </when>
                     <when value="rbf">
-                        <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels"/>
+                        <param name="gamma" type="float" optional="true" label="Gamma Value" help="Kernel coefficient for rbf, poly and sigmoid kernels. Ignored by other kernels" />
                     </when>
-                    <when value="linear"/>
-                    <when value="cosine"/>
-                    <when value="precomputed"/>
+                    <when value="linear" />
+                    <when value="cosine" />
+                    <when value="precomputed" />
                 </conditional>
                 <conditional name="select_solver_type">
                     <param name="eigen_solver_opts" type="select" label="Eigen Solver">
@@ -129,89 +129,89 @@
                         <option value="arpack">arpack</option>
                     </param>
                     <when value="arpack">
-                        <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack"/>
-                        <param name="max_iter" type="integer" optional="true" label="Maximum Iterations" help="Maximum number of iterations for arpack"/>
+                        <param name="tolerance" type="float" value="0.0" label="Tolerance" help="Convergence tolerance for arpack. If 0, optimal value will be chosen by arpack" />
+                        <param name="max_iter" type="integer" optional="true" label="Maximum Iterations" help="Maximum number of iterations for arpack" />
                     </when>
-                    <when value="auto"/>
-                    <when value="dense"/>
+                    <when value="auto" />
+                    <when value="dense" />
                 </conditional>
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="tabular" name="outfile"/>
+        <data format="tabular" name="outfile" />
     </outputs>
     <tests>
         <test>
-            <param name="infile" value="pca_input.dat" ftype="tabular"/>
-            <param name="selected_column_selector_option" value="by_index_number"  />
-            <param name="col1" value="1,2,4,6,8,5"/>
-            <param name="number" value="5"/>
-            <param name="select_pca_opts" value="classical"/>
-            <param name="svd_solver_opts" value="arpack"/>
-            <param name="tolerance" value="0.4"/>
-            <output name="outfile" ftype='tabular' file="pca_classical_output.dat"/>
+            <param name="infile" value="pca_input.dat" ftype="tabular" />
+            <param name="selected_column_selector_option" value="by_index_number" />
+            <param name="col1" value="1,2,4,6,8,5" />
+            <param name="number" value="5" />
+            <param name="select_pca_opts" value="classical" />
+            <param name="svd_solver_opts" value="arpack" />
+            <param name="tolerance" value="0.4" />
+            <output name="outfile" ftype='tabular' file="pca_classical_output.dat" />
         </test>
         <test>
-            <param name="infile" value="pca_input_with_headers.dat" ftype="tabular"/>
-            <param name="header" value="--header"/>
-            <param name="selected_column_selector_option" value="by_header_name"  />
-            <param name="col1" value="col_1,col_2,col_4,col_6,col_8,col_5"/>
-            <param name="number" value="5"/>
-            <param name="select_pca_opts" value="classical"/>
-            <param name="svd_solver_opts" value="arpack"/>
-            <param name="tolerance" value="0.4"/>
-            <output name="outfile" ftype='tabular' file="pca_classical_header_names_output.dat"/>
+            <param name="infile" value="pca_input_with_headers.dat" ftype="tabular" />
+            <param name="header" value="--header" />
+            <param name="selected_column_selector_option" value="by_header_name" />
+            <param name="col1" value="col_1,col_2,col_4,col_6,col_8,col_5" />
+            <param name="number" value="5" />
+            <param name="select_pca_opts" value="classical" />
+            <param name="svd_solver_opts" value="arpack" />
+            <param name="tolerance" value="0.4" />
+            <output name="outfile" ftype='tabular' file="pca_classical_header_names_output.dat" />
         </test>
         <test>
-            <param name="infile" value="pca_input.dat" ftype="tabular"/>
-            <param name="selected_column_selector_option" value="all_but_by_index_number"/>
+            <param name="infile" value="pca_input.dat" ftype="tabular" />
+            <param name="selected_column_selector_option" value="all_but_by_index_number" />
             <param name="col1" value="8,5" />
-            <param name="number" value="7"/>
-            <param name="select_pca_opts" value="incremental"/>
-            <param name="batch_size" value="64"/>
-            <output name="outfile" ftype='tabular' file="pca_incremental_output.dat"/>
+            <param name="number" value="7" />
+            <param name="select_pca_opts" value="incremental" />
+            <param name="batch_size" value="64" />
+            <output name="outfile" ftype='tabular' file="pca_incremental_output.dat" />
         </test>
         <test>
-            <param name="infile" value="pca_input_with_headers.dat" ftype="tabular"/>
-            <param name="header" value="--header"/>
-            <param name="selected_column_selector_option" value="all_but_by_header_name"  />
-            <param name="col1" value="col_8,col_5"/>
-            <param name="number" value="7"/>
-            <param name="select_pca_opts" value="incremental"/>
-            <param name="batch_size" value="64"/>
-            <output name="outfile" ftype='tabular' file="pca_incremental_header_names_output.dat"/>
+            <param name="infile" value="pca_input_with_headers.dat" ftype="tabular" />
+            <param name="header" value="--header" />
+            <param name="selected_column_selector_option" value="all_but_by_header_name" />
+            <param name="col1" value="col_8,col_5" />
+            <param name="number" value="7" />
+            <param name="select_pca_opts" value="incremental" />
+            <param name="batch_size" value="64" />
+            <output name="outfile" ftype='tabular' file="pca_incremental_header_names_output.dat" />
         </test>
         <test>
-            <param name="infile" value="pca_input.dat" ftype="tabular"/>
-            <param name="selected_column_selector_option" value="all_columns"  />
-            <param name="number" value="8"/>
-            <param name="select_pca_opts" value="kernel"/>
-            <param name="kernel_opts" value="linear"/>
-            <param name="eigen_solver_opts" value="arpack"/>
-            <param name="tolerance" value="4.3"/>
-            <param name="max_iter" value="8"/>
+            <param name="infile" value="pca_input.dat" ftype="tabular" />
+            <param name="selected_column_selector_option" value="all_columns" />
+            <param name="number" value="8" />
+            <param name="select_pca_opts" value="kernel" />
+            <param name="kernel_opts" value="linear" />
+            <param name="eigen_solver_opts" value="arpack" />
+            <param name="tolerance" value="4.3" />
+            <param name="max_iter" value="8" />
             <output name="outfile" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="300"/>
-                    <has_n_columns n="8"/>
+                    <has_n_lines n="300" />
+                    <has_n_columns n="8" />
                 </assert_contents>
             </output>
         </test>
         <test>
-            <param name="infile" value="pca_input.dat" ftype="tabular"/>
-            <param name="selected_column_selector_option" value="all_columns"  />
-            <param name="number" value="8"/>
-            <param name="select_pca_opts" value="kernel"/>
-            <param name="kernel_opts" value="poly"/>
-            <param name="gamma" value="0.3"/>
-            <param name="degree" value="4"/>
-            <param name="coef0" value="1.6"/>
-            <param name="eigen_solver_opts" value="auto"/>
+            <param name="infile" value="pca_input.dat" ftype="tabular" />
+            <param name="selected_column_selector_option" value="all_columns" />
+            <param name="number" value="8" />
+            <param name="select_pca_opts" value="kernel" />
+            <param name="kernel_opts" value="poly" />
+            <param name="gamma" value="0.3" />
+            <param name="degree" value="4" />
+            <param name="coef0" value="1.6" />
+            <param name="eigen_solver_opts" value="auto" />
             <output name="outfile" ftype="tabular">
                 <assert_contents>
-                    <has_n_lines n="300"/>
-                    <has_n_columns n="8"/>
+                    <has_n_lines n="300" />
+                    <has_n_columns n="8" />
                 </assert_contents>
             </output>
         </test>
@@ -222,9 +222,10 @@
 **What it does**
 
 This tool takes a tabular input file (one data point per row, each column a variable)
-and performs PCA using Singular Value Decomposition, returning an equally sized tabular
-file with the first PC in the first column, second PC in the second column, etc.
+and performs principal component analysis (PCA) using Singular Value Decomposition,
+returning an equally sized tabular file with the first PC in the first column, second
+PC in the second column, etc.
         ]]>
     </help>
-    <expand macro="sklearn_citation"/>
+    <expand macro="sklearn_citation" />
 </tool>