# HG changeset patch
# User devteam
# Date 1611568812 0
# Node ID 13b6f0007d9e2c7a4fd18e8f49f008fcc05c5ce3
# Parent  9cd341095afde596b0e6599fdfebcd9e1b4fc74f
"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/column_maker commit 35c79ccee143e8d178ebd24f6317888de3ca0187"

diff -r 9cd341095afd -r 13b6f0007d9e column_maker.py
--- a/column_maker.py	Wed Dec 30 00:50:15 2020 +0000
+++ b/column_maker.py	Mon Jan 25 10:00:12 2021 +0000
@@ -9,17 +9,22 @@
 import argparse
 import json
 import re
+import sys
 
 parser = argparse.ArgumentParser()
 parser.add_argument('input', type=argparse.FileType('r'), help="input file")
 parser.add_argument('output', type=argparse.FileType('wt'), help="output file")
 parser.add_argument('cond', nargs='?', type=str, help="expression")
-parser.add_argument('round', nargs='?', type=str, choices=['yes', 'no'],
-                    help="round result")
 parser.add_argument('columns', nargs='?', type=int, help="number of columns")
 parser.add_argument('column_types', nargs='?', type=str, help="comma separated list of column types")
-parser.add_argument('avoid_scientific_notation', nargs='?', type=str, choices=['yes', 'no'],
+parser.add_argument('--round', action="store_true",
+                    help="round result")
+parser.add_argument('--avoid_scientific_notation', action="store_true",
                     help="avoid scientific notation")
+parser.add_argument('--header_new_column_name', default=None, type=str,
+                    help="First line of input is a header line with column "
+                         "names and this should become the name of the new "
+                         "column")
 parser.add_argument('--load_json', default=None, type=argparse.FileType('r'),
                     help="overwrite parsed arguments from json file")
 args = parser.parse_args()
@@ -33,42 +38,40 @@
 out = argparse_dict['output']
 expr = argparse_dict['cond']
 round_result = argparse_dict['round']
+avoid_scientific_notation = argparse_dict['avoid_scientific_notation']
+
+if argparse_dict['header_new_column_name'] is not None:
+    header_line = fh.readline().strip('\n')
+    out.write(
+        '{0}\t{1}\n'.format(
+            header_line, argparse_dict['header_new_column_name']
+        )
+    )
 try:
     in_columns = int(argparse_dict['columns'])
+    if in_columns < 2:
+        # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
+        raise ValueError
 except Exception:
-    exit("Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
-if in_columns < 2:
-    # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
-    exit("Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
+    if not fh.readline():
+        # empty file content is ok and should produce empty output
+        out.close()
+        sys.exit()
+    sys.exit("Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
 try:
     in_column_types = argparse_dict['column_types'].split(',')
 except Exception:
-    exit("Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
+    sys.exit("Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
 if len(in_column_types) != in_columns:
-    exit("The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
-avoid_scientific_notation = argparse_dict['avoid_scientific_notation']
-
-# Unescape if input has been escaped
-mapped_str = {
-    '__lt__': '<',
-    '__le__': '<=',
-    '__eq__': '==',
-    '__ne__': '!=',
-    '__gt__': '>',
-    '__ge__': '>=',
-    '__sq__': '\'',
-    '__dq__': '"',
-}
-for key, value in mapped_str.items():
-    expr = expr.replace(key, value)
+    sys.exit("The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data.")
 
 operators = 'is|not|or|and'
 builtin_and_math_functions = 'abs|all|any|bin|chr|cmp|complex|divmod|float|bool|hex|int|len|long|max|min|oct|ord|pow|range|reversed|round|sorted|str|sum|type|unichr|unicode|log|log10|exp|sqrt|ceil|floor'
 string_and_list_methods = [name for name in dir('') + dir([]) if not name.startswith('_')]
 whitelist = r"^([c0-9\+\-\*\/\(\)\.\'\"><=,:! ]|%s|%s|%s)*$" % (operators, builtin_and_math_functions, '|'.join(string_and_list_methods))
 if not re.compile(whitelist).match(expr):
-    exit("Invalid expression")
-if avoid_scientific_notation == "yes":
+    sys.exit("Invalid expression")
+if avoid_scientific_notation:
     expr = "format_float_positional(%s)" % expr
 
 # Prepare the column variable names and wrappers for column data types
@@ -77,7 +80,7 @@
     col_name = "c%d" % col
     cols.append(col_name)
     col_type = in_column_types[col - 1].strip()
-    if round_result == 'no' and col_type == 'int':
+    if not round_result and col_type == 'int':
         col_type = 'float'
     type_cast = "%s(%s)" % (col_type, col_name)
     type_casts.append(type_cast)
@@ -118,7 +121,7 @@
         %s
         %s
         new_val = %s
-        if round_result == "yes":
+        if round_result:
             new_val = int(round(new_val))
         new_line = line + '\\t' + str(new_val) + "\\n"
         out.write(new_line)
@@ -138,9 +141,9 @@
     out.close()
     if str(e).startswith('invalid syntax'):
         valid_expr = False
-        exit('Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr)
+        sys.exit('Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr)
     else:
-        exit(str(e))
+        sys.exit(str(e))
 
 if valid_expr:
     out.close()
diff -r 9cd341095afd -r 13b6f0007d9e column_maker.xml
--- a/column_maker.xml	Wed Dec 30 00:50:15 2020 +0000
+++ b/column_maker.xml	Mon Jan 25 10:00:12 2021 +0000
@@ -1,45 +1,52 @@
-<tool id="Add_a_column1" name="Compute" version="1.4">
+<tool id="Add_a_column1" name="Compute" version="1.5">
     <description>an expression on every row</description>
     <requirements>
         <requirement type="package" version="3.8">python</requirement>
-        <requirement type="package" version="4.4">sed</requirement>
         <requirement type="package" version="1.19.1">numpy</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-        #if $header_lines_conditional.header_lines_select == "yes":
-            (sed -n '1,1p' '$input' | sed  "s|$|%${header_lines_conditional.header_new_column_name}|" | tr "%" "\t") > header &&
-            sed '1,1d' '$input' > data &&
-        #else:
-            touch header &&
-            ln -s '$input' data &&
-        #end if
+        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'))
 
         python '$__tool_directory__/column_maker.py'
-             data column_maker_output
+             data '$out_file1'
              --load_json '$inputs'
-        && cat header column_maker_output > '$out_file1'
     ]]></command>
     <configfiles>
       <inputs name="inputs"/>
     </configfiles>
     <inputs>
-        <param name="cond" type="text" value="c3-c2" label="Add expression"/>
+        <param name="cond" type="text" value="c3-c2" label="Add expression">
+            <sanitizer>
+                <valid initial="default">
+                    <add value="&lt;" />
+                    <add value="&gt;" />
+                    <add value="&quot;" />
+                    <add value="&apos;" />
+                </valid>
+            </sanitizer>
+        </param>
         <param format="tabular" name="input" type="data" label="as a new column to" help="Dataset missing? See TIP below"/>
-        <param name="round" type="select" label="Round result?">
-            <option value="no">NO</option>
-            <option value="yes">YES</option>
-        </param>
+        <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"
+        help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers)." />
         <conditional name="header_lines_conditional">
-            <param name="header_lines_select" type="select" label="Skip a header line" help="# characters are already considered as comments and kept" >
-                <option value="no" >no</option>
-                <option value="yes" >yes</option>
+            <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>
             </param>
             <when value="no">
             </when>
@@ -47,10 +54,6 @@
                 <param name="header_new_column_name" type="text" value="New Column" label="The new column name" />
             </when>
         </conditional>
-        <param name="avoid_scientific_notation" type="select" label="Avoid scientific notation" help="If yes, use fully expanded decimal representation when writing new columns (use only if expression produces decimal numbers).">
-            <option value="no">no</option>
-            <option value="yes">yes</option>
-        </param>
     </inputs>
     <outputs>
         <data format_source="input" name="out_file1" metadata_source="input"/>
@@ -59,19 +62,19 @@
         <test>
             <param name="cond" value="c3-c2"/>
             <param name="input" value="1.bed"/>
-            <param name="round" value="no"/>
+            <param name="round" value="false"/>
             <output name="out_file1" file="column_maker_out1.interval"/>
         </test>
         <test>
             <param name="cond" value="c4*1"/>
             <param name="input" value="1.interval"/>
-            <param name="round" value="no"/>
+            <param name="round" value="false"/>
             <output name="out_file1" file="column_maker_out2.interval"/>
         </test>
         <test>
             <param name="cond" value="c4*1"/>
             <param name="input" value="1.header.tsv"/>
-            <param name="round" value="no"/>
+            <param name="round" value="false"/>
             <conditional name="header_lines_conditional">
                 <param name="header_lines_select" value="yes" />
                 <param name="header_new_column_name" value="value1_again" />
@@ -81,13 +84,13 @@
         <test>
             <param name="cond" value="c4*1"/>
             <param name="input" value="1.interval"/>
-            <param name="round" value="yes"/>
+            <param name="round" value="true"/>
             <output name="out_file1" file="column_maker_out3.interval"/>
         </test>
         <test>
             <param name="cond" value="float(.0000000000001)"/>
             <param name="input" value="1.bed"/>
-            <param name="round" value="no"/>
+            <param name="round" value="false"/>
             <output name="out_file1">
                 <assert_contents>
                     <has_text text="CCDS10397" />
@@ -98,8 +101,8 @@
         <test>
             <param name="cond" value="float(.0000000000001)"/>
             <param name="input" value="1.bed"/>
-            <param name="round" value="no"/>
-            <param name="avoid_scientific_notation" value="yes"/>
+            <param name="round" value="false"/>
+            <param name="avoid_scientific_notation" value="true"/>
             <output name="out_file1">
                 <assert_contents>
                     <has_text text="CCDS10397" />