comparison main_macros.xml @ 1:d938b80a954f draft

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

0:dac8a9712939

          <option value="k-means++">k-means++</option>
          <option value="random">random</option>
      </param>
  </xml>

  <xml name="multiple_sparse">
    <repeat name="sparse_inputs" min="1" max="10" title="Inputs">
        <param name="input" type="data" format="txt" label="Sparse matrix file (.mtx, .txt)" help="Specify a sparse matrix file in .txt format."/>
    </repeat>
  </xml>

  <xml name="eden_citation">
    <citations>
        <citation type="bibtex">
            @misc{fabrizio_costa_2015_15094,

      <when value="MiniBatchKMeans">
          <expand macro="minibatch_kmeans_advanced_options"/>
      </when>
    </conditional>
  </xml>
</macros>

1:d938b80a954f

          <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,

      <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>