diff main_macros.xml @ 4:c85acc0197c6 draft

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

--- a/main_macros.xml	Fri Jun 03 13:55:59 2016 -0400
+++ b/main_macros.xml	Thu Jun 23 15:26:05 2016 -0400
@@ -1,6 +1,16 @@
 <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>
@@ -219,12 +229,12 @@
   </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>
+    <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>
 
@@ -248,6 +258,43 @@
     <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@"/>