comparison main_macros.xml @ 5:4338e8aac25b draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit a9f28163f0d2e808e49c43a6df5a040706e79991

4:3df106e75b33

<macros>
  <token name="@VERSION@">0.9</token>

  <xml name="python_requirements">
    <requirements>
        <requirement type="package" version="0.2.1b">eden</requirement>
        <yield />

  <xml name="pos_label" token_default_value="">
    <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
  </xml>

  <xml name="average">
    <param argument="average" type="select" optional="True" label="Averaging type" help=" ">
      <option value="binary" selected="true" help="Only report results for the class specified by pos_label. Applicable only on binary classification.">binary</option>
      <option value="micro" help="Calculate metrics globally by counting the total true positives, false negatives and false positives.">micro</option>
      <option value="samples" help="Calculate metrics for each instance, and find their average (only meaningful for multilabel).">samples</option>
      <!--option value="macro" help=""></option-->
      <!--option value="weighted" help=""></option-->
    </param>
  </xml>

  <xml name="beta">
    <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>

    <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
    <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
    <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
    <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
    <yield/>
  </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@"/>

5:4338e8aac25b

<macros>
  <token name="@VERSION@">0.9</token>

  <token name="@COLUMNS_FUNCTION@">
def columns(f,c):
  data = pandas.read_csv(f, sep='\t', header=None, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False)
  cols = c.split (',')
  cols = map(int, cols)
  cols = list(map(lambda x: x - 1, cols))
  y = data.iloc[:,cols].values
  return y
  </token>

  <xml name="python_requirements">
    <requirements>
        <requirement type="package" version="0.2.1b">eden</requirement>
        <yield />

  <xml name="pos_label" token_default_value="">
    <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
  </xml>

  <xml name="average">
    <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
      <option value="micro" help="Calculate metrics globally by counting the total true positives, false negatives and false positives.">micro</option>
      <option value="samples" help="Calculate metrics for each instance, and find their average (only meaningful for multilabel).">samples</option>
      <!--option value="macro" help=""></option-->
      <!--option value="weighted" help=""></option-->
      <yield/>
    </param>
  </xml>

  <xml name="beta">
    <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>

    <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
    <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
    <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
    <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
    <yield/>
  </xml>


  <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
    <conditional name="true_columns">
      <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
          <option value="tabular" selected="true">Tabular</option>
          <option value="sparse">Sparse</option>
      </param>
      <when value="tabular">
        <param name="infile1" type="data" label="@LABEL1@"/>
        <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/>
      </when>
      <when value="sparse">
          <param name="infile1" type="data" format="txt" label="@LABEL1@"/>
      </when>
    </conditional>
    <conditional name="predicted_columns">
      <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
          <option value="tabular" selected="true">Tabular</option>
          <option value="sparse">Sparse</option>
      </param>
      <when value="tabular">
        <param name="infile2" type="data" label="@LABEL2@"/>
        <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
      </when>
      <when value="sparse">
          <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
      </when>
    </conditional>
  </xml>

  <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False">
    <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
    <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select the target column:"/>
    <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
    <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
  </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@"/>