changeset 2:6f05390deffa draft

"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/pandas_pivot_table/ commit 1ca7433aaa606c636f796c75b6cfd8a080e2d5bc-dirty"

--- a/pandas_pivot_table.py	Wed Dec 16 16:13:51 2020 +0000
+++ b/pandas_pivot_table.py	Wed Dec 16 17:44:58 2020 +0000
@@ -58,6 +58,11 @@
         default=None,
         help='fill value for missing values'
     )
+    p.add_argument(
+        '-f', '--float_format',
+        default='%0.6f',
+        help=''
+    )
     args = p.parse_args()
 
     def getValueType(val):
@@ -128,7 +133,10 @@
                          fill_value=fill_value)
     pdf_cols = ['_'.join(reversed(p)) if isinstance(p, tuple) else p
                 for p in pdf.columns.tolist()]
-    pdf.to_csv(args.output, sep='\t', float_format='%0.6f', header=pdf_cols)
+    pdf.to_csv(args.output,
+               sep='\t',
+               float_format=args.float_format,
+               header=pdf_cols)
 
 
 if __name__ == "__main__":

--- a/pandas_pivot_table.xml	Wed Dec 16 16:13:51 2020 +0000
+++ b/pandas_pivot_table.xml	Wed Dec 16 17:44:58 2020 +0000
@@ -20,6 +20,12 @@
         --columns '$pvt_columns'
         --values '$pvt_values'
         --aggfunc='$aggfunc'
+        #if $fill_value
+            --fill_value '$fill_value'
+        #end if
+        #if $float_format
+            --float_format '$float_format'
+        #end if
         --input '$input'
         --output '$output'
     ]]></command>
@@ -58,9 +64,10 @@
               <ul>
               <li>A single function applied to each <i>value</i> column:  <b>"min"</b></li>
               <li>An array of functions applied to each <i>value</i> column:  <b>["min", "max", "mean", "std"]</b></li>
-              <li>A dictionary of <i>value column : functions</i>: <b>{"A" : "sum", "B" : ["min", "max"]}</b></li>
+              <li>A dictionary of <i>value column : function(s)</i>: <b>{"A" : "sum", "B" : ["min", "max"]}</b></li>
               </ul>
             ]]></help>
+            <validator type="regex" message="Do not forget the double quotes">.*".+".*</validator>
             <sanitizer>
                 <valid initial="string.printable">
                    <remove value="&apos;"/>
@@ -70,6 +77,25 @@
                 </mapping>
             </sanitizer>
         </param> 
+	<param name="fill_value" type="text" value="" optional="true" label="Fill value (optional)"
+            help="Value to replace missing values with (in the resulting pivot table, after aggregation) default is an empty field"/>
+	<param name="float_format" type="text" value="" optional="true" label="Output floating point format (optional)">
+            <help>Default is six decimal places: %0.6f</help>
+            <validator type="regex" message="">^%\d+.\d+[fFeEgGn]$</validator>
+            <sanitizer>
+                <valid initial="string.digits">
+                     <add value="%" />
+                     <add value="." />
+                     <add value="f" />
+                     <add value="e" />
+                     <add value="g" />
+                     <add value="F" />
+                     <add value="E" />
+                     <add value="G" />
+                     <add value="n" />
+                 </valid>
+            </sanitizer>
+        </param> 
     </inputs>
     <outputs>
         <data name="output" format="tabular"/>