diff main_macros.xml @ 0:18afd0c1cc56 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/main_macros.xml	Wed May 04 13:09:52 2016 -0400
@@ -0,0 +1,445 @@
+<macros>
+  <token name="@VERSION@">0.9</token>
+
+  <xml name="python_requirements">
+    <requirements>
+        <requirement type="package" version="0.2.1b">eden</requirement>
+        <yield />
+    </requirements>
+  </xml>
+
+  <xml name="macro_stdio">
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+  </xml>
+
+  <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt">
+    <conditional name="selected_tasks">
+        <param name="selected_task" type="select" label="Select a Classification Task">
+            <option value="load">Load a model and predict</option>
+            <option value="train" selected="true">Train a model</option>
+        </param>
+        <when value="load">
+            <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file." />
+            <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
+            <conditional name="prediction_options">
+                <param name="prediction_option" type="select" label="Select the type of prediction">
+                    <option value="predict">Predict class labels</option>
+                    <option value="advanced">Include advanced options</option>
+                </param>
+                <when value="predict">
+                </when>
+                <when value="advanced">
+                </when>
+            </conditional>
+        </when>
+        <when value="train">
+            <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)" />
+            <conditional name="selected_algorithms">
+                <yield />
+            </conditional>
+        </when>
+    </conditional>
+  </xml>
+
+  <xml name="advanced_section">
+    <section name="options" title="Advanced Options" expanded="False">
+      <yield />
+    </section>
+  </xml>
+
+  <xml name="tabular_input">
+    <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
+    <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
+    <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
+  </xml>
+
+  <xml name="tol" token_default_value="0.0" token_help_text="Early stopping heuristics based on the relative center changes. Set to default (0.0) to disable this convergence detection.">
+        <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="n_clusters" token_default_value="8">
+    <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
+  </xml>
+
+  <xml name="fit_intercept" token_checked="true">
+    <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/>
+  </xml>
+
+  <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). ">
+    <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
+    <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="random_state" token_default_value="" token_help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data. A fixed seed allows reproducible results.">
+    <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="warm_start" token_checked="true" token_help_text="When set to True, reuse the solution of the previous call to fit as initialization,otherwise, just erase the previous solution.">
+    <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
+    <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
+  </xml>
+
+  <!--xml name="class_weight" token_default_value="" token_help_text="">
+    <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
+  </xml-->
+
+  <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. ">
+    <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
+    <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
+    <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
+    <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
+      <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
+      <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="n_init" token_default_value="10" >
+      <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
+  </xml>
+
+  <xml name="init">
+      <param argument="init" type="select" label="Centroid initialization method"  help="''k-means++'' selects initial cluster centers that speed up convergence. ''random'' chooses k observations (rows) at random from data as initial centroids.">
+          <option value="k-means++">k-means++</option>
+          <option value="random">random</option>
+      </param>
+  </xml>
+
+  <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
+    <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
+    <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
+  </xml>
+
+  <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
+    <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
+  </xml>    
+
+  <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format.">
+    <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
+        <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
+    </repeat>
+  </xml>  
+
+  <xml name="eden_citation">
+    <citations>
+        <citation type="bibtex">
+            @misc{fabrizio_costa_2015_15094,
+              author       = {Fabrizio Costa and
+                              Björn Grüning and
+                              gigolo},
+              title        = {EDeN: EDeN - Graph Vectorizer},
+              month        = feb,
+              year         = 2015,
+              doi          = {10.5281/zenodo.15094},
+              url          = {http://dx.doi.org/10.5281/zenodo.15094}
+                    }
+                        }
+        </citation>
+    </citations>
+  </xml>
+
+  <xml name="sklearn_citation">
+    <citations>
+        <citation type="bibtex">
+            @article{scikit-learn,
+             title={Scikit-learn: Machine Learning in {P}ython},
+             author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
+                     and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
+                     and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
+                     Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
+             journal={Journal of Machine Learning Research},
+             volume={12},
+             pages={2825--2830},
+             year={2011}
+             url = {https://github.com/scikit-learn/scikit-learn}
+            }
+        </citation>
+    </citations>
+  </xml>
+
+  <xml name="scipy_citation">
+    <citations>
+        <citation type="bibtex">
+          @Misc{,
+          author =    {Eric Jones and Travis Oliphant and Pearu Peterson and others},
+          title =     {{SciPy}: Open source scientific tools for {Python}},
+          year =      {2001--},
+          url = "http://www.scipy.org/",
+          note = {[Online; accessed 2016-04-09]}
+        }
+        </citation>
+    </citations>
+  </xml>
+
+
+  <xml name="nn_advanced_options">
+    <section name="options" title="Advanced Options" expanded="False">
+      <yield/>
+      <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
+          <option value="uniform" selected="true" help="Uniform weights. All points in each neighborhood are weighted equally.">Uniform</option>
+          <option value="distance" help="Weight points by the inverse of their distance.">Distance</option>
+      </param>
+      <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
+          <option value="auto" selected="true">Auto</option>
+          <option value="ball_tree">BallTree</option>
+          <option value="kd_tree">KDTree</option>
+          <option value="brute">Brute-force</option>
+      </param>
+      <param argument="leaf_size" type="integer" value="30" label="Leaf size" help="Used with BallTree and KDTree. Affects the time and memory usage of the constructed tree."/>
+      <!--param name="metric"-->
+      <!--param name="p"-->
+      <!--param name="metric_params"-->
+    </section>
+  </xml>
+
+  <xml name="svc_advanced_options">
+    <section name="options" title="Advanced Options" expanded="False">
+        <yield/>
+        <param argument="kernel" type="select" optional="true" label="Kernel type" help="Kernel type to be used in the algorithm. If none is given, ‘rbf’ will be used.">
+            <option value="rbf" selected="true">rbf</option>
+            <option value="linear">linear</option>
+            <option value="poly">poly</option>
+            <option value="sigmoid">sigmoid</option>
+            <option value="precomputed">precomputed</option>
+        </param>
+        <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
+        <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
+        <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Independent term in kernel function. dafault: 0.0 "/>
+        <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help=" "/>
+        <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
+        <!-- param argument="cache_size"-->
+        <!--expand macro="class_weight"/-->
+        <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/> 
+        <expand macro="max_iter" default_value="-1" label="Solver maximum number of iterations" help_text="Hard limit on iterations within solver, or -1 for no limit."/>
+        <!--param argument="decision_function_shape"-->
+        <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/>
+    </section>
+  </xml>
+
+  <xml name="spectral_clustering_advanced_options">
+    <section name="options" title="Advanced Options" expanded="False">
+        <expand macro="n_clusters"/>
+        <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
+            <option value="arpack" selected="true">arpack</option>
+            <option value="lobpcg">lobpcg</option>
+            <option value="amg">amg</option>
+            <!--None-->
+        </param>
+        <expand macro="random_state"/>
+        <expand macro="n_init"/>
+        <param argument="gamma" type="float" optional="true" value="1.0" label="Kernel scaling factor" help="Scaling factor of RBF, polynomial, exponential chi^2 and sigmoid affinity kernel. Ignored for affinity=''nearest_neighbors''."/>
+        <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
+            <option value="rbf" selected="true">RBF</option>
+            <option value="precomputed">precomputed</option>
+            <option value="nearest_neighbors">Nearset neighbors</option>
+        </param>
+        <param argument="n_neighbors" type="integer" optional="true" value="10" label="Number of neighbors" help="Number of neighbors to use when constructing the affinity matrix using the nearest neighbors method. Ignored for affinity=''rbf''"/>
+        <!--param argument="eigen_tol"-->
+        <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
+            <option value="kmeans" selected="true">kmeans</option>
+            <option value="discretize">discretize</option>
+        </param>
+        <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
+        <param argument="coef0" type="integer" optional="true" value="1" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
+        <!--param argument="kernel_params"-->
+    </section>
+  </xml>
+
+  <xml name="minibatch_kmeans_advanced_options">
+    <section name="options" title="Advanced Options" expanded="False">
+        <expand macro="n_clusters"/>
+        <expand macro="init"/>
+        <expand macro="n_init" default_value="3"/>
+        <expand macro="max_iter" default_value="100"/>
+        <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/> 
+        <expand macro="random_state"/>
+        <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
+        <!--param argument="compute_labels"-->
+        <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
+        Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
+        To disable, set max_no_improvement to None. "/>
+        <param argument="init_size" type="integer" optional="true" value="" label="Number of random initialization samples" help="Number of samples to randomly sample for speeding up the initialization . ( default: 3 * batch_size )"/>
+        <param argument="reassignment_ratio" type="float" optional="true" value="0.01" label="Re-assignment ratio" help="Controls the fraction of the maximum number of counts for a center to be reassigned. Higher values yield better clustering results."/>
+    </section>
+  </xml>
+
+  <xml name="kmeans_advanced_options">
+    <section name="options" title="Advanced Options" expanded="False">
+      <expand macro="n_clusters"/>
+      <expand macro="init"/>
+      <expand macro="n_init"/>
+      <expand macro="max_iter"/>
+      <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
+      <!--param argument="precompute_distances"/-->
+      <expand macro="random_state"/>
+      <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing distances" help="Mofifying the original data introduces small numerical differences caused by subtracting and then adding the data mean."/>
+    </section>
+  </xml>
+
+  <xml name="birch_advanced_options">
+    <section name="options" title="Advanced Options" expanded="False">
+      <param argument="threshold" type="float" optional="true" value="0.5" label="Subcluster radius threshold" help="The radius of the subcluster obtained by merging a new sample; the closest subcluster should be less than the threshold to avoid a new subcluster."/>
+      <param argument="branching_factor" type="integer" optional="true" value="50" label="Maximum number of subclusters per branch" help="Maximum number of CF subclusters in each node."/>
+      <expand macro="n_clusters" default_value="3"/>
+      <!--param argument="compute_labels"/-->
+    </section>
+  </xml>
+
+  <xml name="dbscan_advanced_options">
+    <section name="options" title="Advanced Options" expanded="False">
+      <param argument="eps" type="float" optional="true" value="0.5" label="Maximum neighborhood distance" help="The maximum distance between two samples for them to be considered as in the same neighborhood."/>
+      <param argument="min_samples" type="integer" optional="true" value="5" label="Minimal core point density" help="The number of samples (or total weight) in a neighborhood for a point (including the point itself) to be considered as a core point."/>
+      <param argument="metric" type="text" optional="true" value="euclidean" label="Metric" help="The metric to use when calculating distance between instances in a feature array."/>
+      <param argument="algorithm" type="select" label="Pointwise distance computation algorithm" help="The algorithm to be used by the NearestNeighbors module to compute pointwise distances and find nearest neighbors.">
+          <option value="auto" selected="true">auto</option>
+          <option value="ball_tree">ball_tree</option>
+          <option value="kd_tree">kd_tree</option>
+          <option value="brute">brute</option>
+      </param>
+      <param argument="leaf_size" type="integer" optional="true" value="30" label="Leaf size" help="Leaf size passed to BallTree or cKDTree. Memory and time efficieny factor in tree constrution and querying."/>
+    </section>
+  </xml>
+
+  <xml name="clustering_algorithms_options">
+    <conditional name="algorithm_options">
+      <param name="selected_algorithm" type="select" label="Clustering Algorithm">
+          <option value="KMeans" selected="true">KMeans</option>
+          <option value="SpectralClustering">Spectral Clustering</option>
+          <option value="MiniBatchKMeans">Mini Batch KMeans</option>
+          <option value="DBSCAN">DBSCAN</option>
+          <option value="Birch">Birch</option>
+      </param>
+      <when value="KMeans">
+          <expand macro="kmeans_advanced_options"/>
+      </when>
+      <when value="DBSCAN">
+          <expand macro="dbscan_advanced_options"/>
+      </when>
+      <when value="Birch">
+          <expand macro="birch_advanced_options"/>
+      </when>
+      <when value="SpectralClustering">
+          <expand macro="spectral_clustering_advanced_options"/>
+      </when>
+      <when value="MiniBatchKMeans">
+          <expand macro="minibatch_kmeans_advanced_options"/>
+      </when>
+    </conditional>
+  </xml>
+
+  <xml name="distance_metrics">
+    <param argument="metric" type="select" label="Distance metric" help=" ">
+      <option value="euclidean" selected="true">euclidean</option>
+      <option value="cityblock">cityblock</option>
+      <option value="cosine">cosine</option>
+      <option value="l1">l1</option>
+      <option value="l2">l2</option>
+      <option value="manhattan">manhattan</option>
+      <yield/>
+    </param>
+  </xml>
+
+  <xml name="distance_nonsparse_metrics">
+    <option value="braycurtis">braycurtis</option>
+    <option value="canberra">canberra</option>
+    <option value="chebyshev">chebyshev</option>
+    <option value="correlation">correlation</option>
+    <option value="dice">dice</option>
+    <option value="hamming">hamming</option>
+    <option value="jaccard">jaccard</option>
+    <option value="kulsinski">kulsinski</option>
+    <option value="mahalanobis">mahalanobis</option>
+    <option value="matching">matching</option>
+    <option value="minkowski">minkowski</option>
+    <option value="rogerstanimoto">rogerstanimoto</option>
+    <option value="russellrao">russellrao</option>
+    <option value="seuclidean">seuclidean</option>
+    <option value="sokalmichener">sokalmichener</option>
+    <option value="sokalsneath">sokalsneath</option>
+    <option value="sqeuclidean">sqeuclidean</option>
+    <option value="yule">yule</option>
+  </xml>
+
+  <xml name="pairwise_kernel_metrics">
+    <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
+      <option value="rbf" selected="true">rbf</option>
+      <option value="sigmoid">sigmoid</option>
+      <option value="polynomial">polynomial</option>
+      <option value="linear" selected="true">linear</option>
+      <option value="chi2">chi2</option>
+      <option value="additive_chi2">additive_chi2</option>
+    </param>
+  </xml>
+
+  <xml name="sparse_pairwise_metric_functions">
+    <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
+      <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
+      <option value="pairwise_distances">Distance matrix</option>
+      <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
+      <yield/>
+    </param>
+  </xml>
+
+  <xml name="pairwise_metric_functions">
+    <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
+    <option value="chi2_kernel">Exponential chi-squared kernel</option>
+    <option value="linear_kernel">Linear kernel</option>
+    <option value="manhattan_distances">L1 distances</option>
+    <option value="pairwise_kernels">Kernel</option>
+    <option value="polynomial_kernel">Polynomial kernel</option>
+    <option value="rbf_kernel">Gaussian (rbf) kernel</option>
+    <option value="laplacian_kernel">Laplacian kernel</option>
+  </xml>
+
+  <xml name="sparse_pairwise_condition">
+    <when value="pairwise_distances">
+      <section name="options" title="Advanced Options" expanded="False">
+          <expand macro="distance_metrics">
+              <yield/>
+          </expand>
+      </section>
+    </when>
+    <when value="euclidean_distances">
+      <section name="options" title="Advanced Options" expanded="False">
+          <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Return squared Euclidean distances" help=" "/>
+      </section>
+    </when>
+  </xml>
+
+  <xml name="argmin_distance_condition">
+    <when value="pairwise_distances_argmin">
+      <section name="options" title="Advanced Options" expanded="False">
+          <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
+          <expand macro="distance_metrics">
+              <yield/>
+          </expand>
+          <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
+      </section>
+    </when>
+  </xml>
+
+</macros>
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