changeset 8:02026300aa45 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker commit 276e05a2c72c031318eef8c57deebbbde822b538"

--- a/column_maker.py	Wed Feb 24 05:20:07 2021 +0000
+++ b/column_maker.py	Tue Mar 09 18:33:10 2021 +0000
@@ -10,14 +10,14 @@
 import json
 import re
 import sys
-# functions that may be used in the compute expression
+# Functions that may be used in the compute expression
 from math import (  # noqa: F401
     ceil,
     exp,
     floor,
     log,
     log10,
-    sqrt
+    sqrt,
 )
 
 from numpy import format_float_positional  # noqa: F401
@@ -141,15 +141,15 @@
 try:
     exec(code)
 except Exception as e:
-    out.close()
     if str(e).startswith('invalid syntax'):
         valid_expr = False
         sys.exit('Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr)
     else:
         sys.exit(str(e))
+finally:
+    out.close()
 
 if valid_expr:
-    out.close()
     valid_lines = total_lines - skipped_lines
     print('Creating column %d with expression %s' % (in_columns + 1, expr))
     if valid_lines > 0:

--- a/column_maker.xml	Wed Feb 24 05:20:07 2021 +0000
+++ b/column_maker.xml	Tue Mar 09 18:33:10 2021 +0000
@@ -5,22 +5,21 @@
         <requirement type="package" version="1.19.1">numpy</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-        ln -s '$input' data &&
+## inject colums and column_types metadata into inputs json
+#import json
+#set inputs_dict = json.load(open($inputs))
+#set inputs_dict['columns'] = $input.metadata.columns
+#set inputs_dict['column_types'] = $input.metadata.column_types
+## flatten conditional
+#if $header_lines_conditional.header_lines_select == "yes":
+    #set inputs_dict['header_new_column_name'] = str($header_lines_conditional.header_new_column_name)
+#end if
+#set x = json.dump($inputs_dict, open($inputs, 'w'))
 
-        ## inject colums and column_types metadata into inputs json
-        #import json
-        #set inputs_dict = json.load(open($inputs))
-        #set inputs_dict['columns'] = $input.metadata.columns
-        #set inputs_dict['column_types'] = $input.metadata.column_types
-        ## flatten conditional
-        #if $header_lines_conditional.header_lines_select == "yes":
-            #set inputs_dict['header_new_column_name'] = str($header_lines_conditional.header_new_column_name)
-        #end if
-        #set x = json.dump($inputs_dict, open($inputs, 'w'))
-
-        python '$__tool_directory__/column_maker.py'
-             data '$out_file1'
-             --load_json '$inputs'
+python '$__tool_directory__/column_maker.py'
+'$input'
+'$out_file1'
+--load_json '$inputs'
     ]]></command>
     <configfiles>
       <inputs name="inputs"/>
@@ -36,7 +35,7 @@
                 </valid>
             </sanitizer>
         </param>
-        <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
+        <param name="input" type="data" format="tabular" label="as a new column to" help="Dataset missing? See TIP below"/>
         <param name="round" type="boolean" truevalue="yes" falsevalue="no" label="Round result?" />
         <param name="avoid_scientific_notation" type="boolean" truevalue="yes" falsevalue="no"
         label="Avoid scientific notation"
@@ -45,18 +44,17 @@
             <param name="header_lines_select" type="select"
             label="Input has a header line with column names?"
             help="Select Yes to be able to specify a name for the new column and have it added to the header line. If you select No, the first line will be treated as a regular line: If it is empty or starts with a # character it will be skipped, otherwise the tool will attempt to compute the specified expression on it." >
-                <option value="no" >No</option>
-                <option value="yes" >Yes</option>
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
             </param>
-            <when value="no">
-            </when>
+            <when value="no" />
             <when value="yes">
                 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format_source="input" name="out_file1" metadata_source="input"/>
+        <data name="out_file1" format_source="input" metadata_source="input"/>
     </outputs>
     <tests>
         <test>
@@ -120,7 +118,6 @@
         </test>
     </tests>
     <help><![CDATA[
-
  .. class:: infomark
 
 **TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert*