diff paracords_plot.xml @ 2:9958188c6195 draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot commit b26c6ec671ec63cce1f86c70e928673ed2c82f82"

--- a/paracords_plot.xml	Wed Oct 10 02:29:28 2018 -0400
+++ b/paracords_plot.xml	Mon Nov 04 12:20:51 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="plotly_parallel_coordinates_plot" name="Parallel Coordinates Plot" version="0.1">
+<tool id="plotly_parallel_coordinates_plot" name="Parallel Coordinates Plot" version="0.2">
     <description>of tabular data</description>
     <requirements>
         <requirement type="package" version="3.6">python</requirement>
@@ -9,15 +9,27 @@
     <command detect_errors="aggressive"><![CDATA[
     python '$__tool_directory__/paracords_plot.py'
         -i '$infile'
-        -d '$col_dimensions'
+        -m '$dimension_selections.selected_mode'
+        -d '$dimension_selections.col_dimensions'
         -t '$categorized_datatype'
         -c '$col_color'
 ]]>
     </command>
     <inputs>
-        <param name="infile" type="data" format="tabular" label="Select data file :"/>
-        <param name="col_dimensions" multiple="true" type="data_column" data_ref="infile" use_header_names="true" display="checkboxes" label="Select the columns for dimentions:"/>
-        <param name="categorized_datatype" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="All the dimensions in categorized datatype:"/>
+        <param name="infile" type="data" format="tabular" label="Select table data file "/>
+        <conditional name="dimension_selections">
+            <param name="selected_mode" type="select" label="The mode of column selection">
+                <option value="by_index" selected="true">By index</option>
+                <option value="by_name">By column name</option>
+            </param>
+            <when value="by_index">
+                <param name="col_dimensions" multiple="true" type="data_column" data_ref="infile" use_header_names="true" display="checkboxes" label="Select the columns for dimentions:"/>
+            </when>
+            <when value="by_name">
+                <param name="col_dimensions" type="text" value="^param_.*" label="Type the column names" help="Two modes: 1) multiple names separated by comma, e.g. header1,header2, or 2) include `*` to initiate regular expression searches for every column name, for example, ^param_.* will retreive all the headers starting with param_. Note: no mix of the two is supported. Use default sanitizer: string.ascii_letters + string.digits + &quot; -=_.()/+*^,:?!&quot;)"/>
+            </when>
+        </conditional>
+        <param name="categorized_datatype" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Cast all the dimensions into categorical datatype?"/>
         <param name="col_color" type="data_column" data_ref="infile" use_header_names="true" label="Select a column containg the values for coloring:" help="e.g. mean_test_score"/>
     </inputs>
 
@@ -39,6 +51,14 @@
             <param name="col_color" value="3"/>
             <output name="output" file="parcoords_plot02.html" compare="sim_size"/>
         </test>
+        <test>
+            <param name="infile" value="parcoords02.tabular" ftype="tabular"/>
+            <param name="selected_mode" value="by_name"/>
+            <param name="col_dimensions" value="param_*"/>
+            <param name="categorized_datatype" value="false"/>
+            <param name="col_color" value="3"/>
+            <output name="output" file="parcoords_plot02.html" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[
 **What it does**
@@ -51,4 +71,14 @@
 
     ]]>
     </help>
+    <citations>
+         <citation type="bibtex">
+          @online{plotly,
+          author = {Plotly Technologies Inc.},
+          title = {Collaborative data science},
+          publisher = {Plotly Technologies Inc.},
+          address = {Montreal, QC}, year = {2015},
+          url = {https://plot.ly} }
+        </citation>
+    </citations>
 </tool>