# HG changeset patch
# User iuc
# Date 1568400881 14400
# Node ID 02c3e335a695ac1ede92fc9f4925e8f88f13c2f9
# Parent  dddadbbac949df48c789ad3100194d707b2d43ba
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"

diff -r dddadbbac949 -r 02c3e335a695 scripts/safety.py
--- a/scripts/safety.py	Fri Aug 30 05:28:18 2019 -0400
+++ b/scripts/safety.py	Fri Sep 13 14:54:41 2019 -0400
@@ -11,7 +11,6 @@
         '(', ')', 'if', 'else', 'or', 'and', 'not', 'in',
         '+', '-', '*', '/', '%', ',', '!=', '==', '>', '>=', '<', '<=',
         'min', 'max', 'sum',
-        'str', 'int', 'float'
     )
     __allowed_ref_types = {
         'pd.DataFrame': {
@@ -177,12 +176,13 @@
         # ['vec.median', '(', ')', '+', 'vec.sum', '(', ')']
         tokens = [
             e for e in re.split(
-                r'("[a-zA-Z%0-9_.]+"|[a-zA-Z0-9_.]+|[^a-zA-Z0-9_.() ]+|[()])', self.expr
+                r'([a-zA-Z0-9_.]+|[^a-zA-Z0-9_.() ]+|[()])', self.expr
             ) if e.strip()
         ]
 
         # 2. Subtract allowed standard tokens
         rem = [e for e in tokens if e not in self.__allowed_tokens]
+
         # 3. Subtract allowed qualified objects from allowed modules
         #    and whitelisted references and their attributes
         rem2 = []
@@ -194,32 +194,18 @@
             if len(parts) == 2:
                 if parts[0] in self.these:
                     parts[0] = '_this'
-                elif parts[0] == "":
-                    # e.g. '.T' gives ['','.T']
-                    # Here we assume that the blank part[0] refers to the
-                    # self.ref_type (e.g. "pd.DataFrame"), and that
-                    # the second part is a function of that type.
-                    if parts[1] in self.allowed_qualified['_this']:
-                        continue
-
                 if parts[0] in self.allowed_qualified:
                     if parts[1] in self.allowed_qualified[parts[0]]:
                         continue
-
             rem2.append(e)
 
-        # Debug
-        # for x in (tokens, rem, rem2):print(x)
-
         # 4. Assert that rest are real numbers or strings
         e = ''
         for e in rem2:
             try:
                 _ = float(e)
             except ValueError:
-                # e.g. '"TEXT"' is okay.
-                if not(e[0] == '"' and e[-1] == '"'):
-                    safe = False
-                    break
+                safe = False
+                break
 
         return safe, e
diff -r dddadbbac949 -r 02c3e335a695 scripts/table_compute.py
--- a/scripts/table_compute.py	Fri Aug 30 05:28:18 2019 -0400
+++ b/scripts/table_compute.py	Fri Sep 13 14:54:41 2019 -0400
@@ -4,7 +4,7 @@
 """
 
 
-__version__ = "0.9.1"
+__version__ = "0.9.2"
 
 import csv
 import math
@@ -265,7 +265,12 @@
         mode = params["element_mode"]
         if mode == "replace":
             replacement_val = params["element_replace"]
-            out_table = data.mask(bool_mat, replacement_val)
+            out_table = data.mask(
+                bool_mat,
+                data.where(bool_mat).applymap(
+                    lambda x: replacement_val.format(elem=x)
+                )
+            )
         elif mode == "modify":
             mod_op = Utils.getOneValueMathOp(params["element_modify_op"])
             out_table = data.mask(
@@ -300,7 +305,9 @@
     elif user_mode_single == "fulltable":
         general_mode = params["mode"]
 
-        if general_mode == "melt":
+        if general_mode == "transpose":
+            out_table = data.T
+        elif general_mode == "melt":
             melt_ids = params["MELT"]["melt_ids"]
             melt_values = params["MELT"]["melt_values"]
 
diff -r dddadbbac949 -r 02c3e335a695 table_compute.xml
--- a/table_compute.xml	Fri Aug 30 05:28:18 2019 -0400
+++ b/table_compute.xml	Fri Sep 13 14:54:41 2019 -0400
@@ -1,7 +1,7 @@
 <tool id="table_compute" name="Table Compute" version="@VERSION@">
     <description>computes operations on table data</description>
     <macros>
-        <token name="@VERSION@">0.9.1</token>
+        <token name="@VERSION@">0.9.2</token>
         <token name="@COPEN@"><![CDATA[<code>]]></token>
         <token name="@CCLOSE@"><![CDATA[</code>]]></token>
         <import>allowed_functions.xml</import>
@@ -23,7 +23,7 @@
             <sanitizer sanitize="false" />
         </macro>
         <macro name="validator_functiondef">
-            <validator type="regex" message="An expression is required and is allowed to contain only letters, numbers and the characters '_ !-+=/*%.&lt;&gt;()'">^['"\w !\-+=/*%,.&lt;&gt;()]+$</validator>
+            <validator type="regex" message="An expression is required and is allowed to contain only letters, numbers and the characters _ !-+=/*%.&lt;&gt;()">^[\w !\-+=/*%,.&lt;&gt;()]+$</validator>
             <sanitizer sanitize="false" />
         </macro>
         <!-- macro for main input tests -->
@@ -51,8 +51,9 @@
             <yield />
             <conditional name="user" >
                 <param name="mode" value="element" />
-                <param name="element_op" value="gt" />
-                <param name="element_value" value="0" />
+                <conditional name="elem_val">
+                    <param name="element_op" value="None" />
+                </conditional>
                 <conditional name="element" >
                     <param name="mode" value="custom" />
                     <param name="custom_expr" value="-math.log(1 - elem/4096) * 4096 if elem != 4096 else elem - 0.5" />
@@ -133,6 +134,7 @@
 }
 
 #if str($singtabop.use_type) == "single":
+  #set $op_mode = str($singtabop.user.mode)
 Data = {
     "tables": [
         {
@@ -159,12 +161,12 @@
         }
     ],
     "params": {
-      "user_mode_single": '$singtabop.user.mode.value',
-    #if $singtabop.user.mode.value == 'precision':
+      "user_mode_single": '$op_mode',
+    #if $op_mode == 'precision':
         ## Literally do nothing, the user just sets the precision slider
         ## at the top default level
     }
-    #elif $singtabop.user.mode.value == 'select':
+    #elif $op_mode == 'select':
         "select_cols_unique": #echo 'select_cols_keepdupe' in str($singtabop.user.select_keepdupe)#,
         "select_rows_unique": #echo 'select_rows_keepdupe' in str($singtabop.user.select_keepdupe)#,
       #if $singtabop.user.select_cols_wanted:
@@ -178,24 +180,25 @@
         "select_rows_wanted": None,
       #end if
     }
-    #elif $singtabop.user.mode.value == 'filtersumval':
-        "filtersumval_mode": '$singtabop.user.filtersumval_mode.use.value',
-        "filtersumval_axis": $singtabop.user.axis.value,
-      #if $singtabop.user.filtersumval_mode.use.value == 'operation':
-        "filtersumval_compare": '$singtabop.user.filtersumval_mode.compare_op.value',
-        "filtersumval_op": '$singtabop.user.filtersumval_mode.operation.value',
+    #elif $op_mode == 'filtersumval':
+      #set $filter_type = str($singtabop.user.filtersumval_mode.use)
+        "filtersumval_mode": '$filter_type',
+        "filtersumval_axis": $singtabop.user.axis,
+      #if $filter_type == 'operation':
+        "filtersumval_compare": '$singtabop.user.filtersumval_mode.compare_op',
+        "filtersumval_op": '$singtabop.user.filtersumval_mode.operation',
         "filtersumval_against": $singtabop.user.filtersumval_mode.against,
         "filtersumval_minmatch": None,
-      #elif $singtabop.user.filtersumval_mode.use.value == 'element':
+      #elif $filter_type == 'element':
         "filtersumval_compare": None,
-        "filtersumval_op": '$singtabop.user.filtersumval_mode.operation.value',
+        "filtersumval_op": '$singtabop.user.filtersumval_mode.operation',
         ## against could be string or float, so we parse this in the code
         "filtersumval_against": '$singtabop.user.filtersumval_mode.against',
         "filtersumval_minmatch": $singtabop.user.filtersumval_mode.minmatch,
       #end if
     }
-    #elif $singtabop.user.mode.value == 'matrixapply':
-        "matrixapply_dimension": $singtabop.user.dimension.value,
+    #elif $op_mode == 'matrixapply':
+        "matrixapply_dimension": $singtabop.user.dimension,
       #if str($singtabop.user.matrixapply_func.vector_op) == 'custom':
         #set $custom_func = str($singtabop.user.matrixapply_func.custom_func).strip()
         "matrixapply_custom": True,
@@ -207,10 +210,12 @@
         "matrixapply_op": '$singtabop.user.matrixapply_func.vector_op',
       #end if
     }
-    #elif $singtabop.user.mode.value == 'element':
-      #if str($singtabop.user.elem_val.element_op) == "None":
+    #elif $op_mode == 'element':
+      #set $filter_type = str($singtabop.user.elem_val.element_op)
+      #set $element_mode = str($singtabop.user.element.mode)
+      #if $filter_type == "None":
         "element_op": None,
-      #elif str($singtabop.user.elem_val.element_op) == "rowcol":
+      #elif $filter_type == "rowcol":
         "element_op": "rowcol",
           #if $singtabop.user.elem_val.select_rows_wanted
         "element_rows": '$singtabop.user.elem_val.select_rows_wanted',
@@ -220,24 +225,24 @@
           #end if
         "element_inclusive": $singtabop.user.elem_val.inclusive_selection,
       #else:
-        "element_op": '$singtabop.user.elem_val.element_op.value',
+        "element_op": '$filter_type',
         ## Value is string or float, parsed in code later
         "element_value" : '$singtabop.user.elem_val.element_value',
       #end if
-        "element_mode": '$singtabop.user.element.mode.value',
-      #if str($singtabop.user.element.mode) == "replace":
-        "element_replace": '$singtabop.user.element.replace_value.value',
-      #elif str($singtabop.user.element.mode) == "modify":
-        "element_modify_op": '$singtabop.user.element.modify_op.value',
-      #elif str($singtabop.user.element.mode) == "scale":
-        "element_scale_op": '$singtabop.user.element.scale_op.value',
+        "element_mode": '$element_mode',
+      #if $element_mode == "replace":
+        "element_replace": '$singtabop.user.element.replace_value',
+      #elif $element_mode == "modify":
+        "element_modify_op": '$singtabop.user.element.modify_op',
+      #elif $element_mode == "scale":
+        "element_scale_op": '$singtabop.user.element.scale_op',
         "element_scale_value": $singtabop.user.element.scale_value,
-      #elif str($singtabop.user.element.mode) == "custom":
+      #elif $element_mode == "custom":
         #set $custom_func = str($singtabop.user.element.custom_expr).strip()
         "element_customop": '$custom_func',
       #end if
     }
-    #elif $singtabop.user.mode.value == 'fulltable':
+    #elif $op_mode == 'fulltable':
         "mode": '$singtabop.user.general.use',
       #if str($singtabop.user.general.use) == 'melt':
         #if str($singtabop.user.general.id_vars).strip():
@@ -273,7 +278,7 @@
             "pivot_values": $pivot_values,
         },
       #elif str($singtabop.user.general.use) == 'custom':
-        #set $custom_func = str($singtabop.user.general.fulltable_custom_expr.value).strip()
+        #set $custom_func = str($singtabop.user.general.fulltable_custom_expr).strip()
         "fulltable_customop": '$custom_func',
 
       #end if
@@ -282,7 +287,7 @@
 }
 
 #elif str($singtabop.use_type) == "multiple":
-#set $custom_func = str($singtabop.fulltable_custom_expr).strip()
+  #set $custom_func = str($singtabop.fulltable_custom_expr).strip()
 Data = {
     "tables": [
     #for $i, $s in enumerate($singtabop.tables)
@@ -424,10 +429,12 @@
                     <when value="fulltable">
                         <conditional name="general" >
                             <param name="use" type="select" label="Operation" help="See Examples 5, 7, and 8 for usage" >
-                                <option value="melt" >Melt</option>
-                                <option value="pivot" >Pivot</option>
-                                <option value="custom" >Custom</option>
+                                <option value="transpose">Transpose</option>
+                                <option value="melt">Melt</option>
+                                <option value="pivot">Pivot</option>
+                                <option value="custom">Custom</option>
                             </param>
+                            <when value="transpose" />
                             <when value="melt" >
                                 <param name="id_vars" type="text" value="" label="Variable IDs"
                                        help="Comma-delimited list of column names to use as identifiers" >
@@ -474,7 +481,14 @@
                                 <option value="custom">Custom</option>
                             </param>
                             <when value="replace" >
-                                <param name="replace_value" type="text" label="Replacement value" help="This value is converted to numeric if possible, otherwise it is treated as a string" />
+                                <param name="replace_value" type="text" label="Replacement value" help="If you want to reuse the current value of each element as part of the  replacement value, you can refer to it using the special @COPEN@{elem}@CCLOSE@ placeholder (see Example #9 in the Help section).">
+                                    <sanitizer>
+                                        <valid>
+                                            <add value="{" />
+                                            <add value="}" />
+                                        </valid>
+                                    </sanitizer>
+                                </param>
                             </when>
                             <when value="modify" >
                                 <param name="modify_op" type="select" label="Transformation function" help="Example: to transform values to their square root, select @COPEN@Square Root@CCLOSE@ here.">
@@ -820,7 +834,22 @@
             </expand>
         </test>
         <test expect_num_outputs="1">
-            <!-- Test 22: Melt -->
+            <!-- Test 22: Transpose -->
+            <expand macro="test_inputs_single" >
+                <param name="mode" value="fulltable" />
+                <conditional name="general" >
+                    <param name="use" value="transpose" />
+                </conditional>
+            </expand>
+            <param name="out_opts" value="ignore_nas,output_headers_col" />
+            <output name="table" >
+                <assert_contents>
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- Test 23: Melt -->
             <expand macro="test_inputs_single" >
                 <param name="mode" value="fulltable" />
                 <conditional name="general" >
@@ -839,7 +868,7 @@
             </output>
         </test>
         <test expect_num_outputs="1">
-            <!-- Test 23: Pivot -->
+            <!-- Test 24: Pivot -->
             <expand macro="test_inputs_single" >
                 <param name="mode" value="fulltable" />
                 <conditional name="general" >
@@ -860,7 +889,7 @@
         </test>
         <!-- Add Example Text Tests -->
         <test expect_num_outputs="1" >
-            <!-- Test 24: Ex 1 -->
+            <!-- Test 25: Ex 1 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.1.tsv" />
@@ -881,7 +910,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 25: Ex 2 -->
+            <!-- Test 26: Ex 2 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.2.tsv" />
@@ -906,7 +935,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 26: Ex 3_P1 -->
+            <!-- Test 27: Ex 3_P1 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.3p1.tsv" />
@@ -931,7 +960,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 27: Ex 3_P2 -->
+            <!-- Test 28: Ex 3_P2 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.3p2.tsv" />
@@ -953,7 +982,7 @@
             </output>
 	        </test>
         <test expect_num_outputs="1" >
-            <!-- Test 28: Ex 4 -->
+            <!-- Test 29: Ex 4 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.4.tsv" />
@@ -978,7 +1007,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 29: Ex 5 -->
+            <!-- Test 30: Ex 5 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.5.tsv" />
@@ -1000,7 +1029,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 30: Ex 6 -->
+            <!-- Test 31: Ex 6 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="multiple" />
                 <repeat name="tables" >
@@ -1026,7 +1055,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 31: Ex 7 -->
+            <!-- Test 32: Ex 7 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.7.tsv" />
@@ -1049,7 +1078,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 32: Ex 8 -->
+            <!-- Test 33: Ex 8 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.8.tsv" />
@@ -1073,74 +1102,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 33: Subtracting table means #1 -->
-            <conditional name="singtabop" >
-                <param name="use_type" value="single" />
-                <param name="input" value="examples.5.tsv" />
-                <param name="col_row_names" value="has_col_names,has_row_names" />
-                <conditional name="user" >
-                    <param name="mode" value="fulltable" />
-                    <conditional name="general" >
-                        <param name="use" value="custom" />
-                        <param name="fulltable_custom_expr" value="table - table.mean(1)/table.std(1)" />
-                    </conditional>
-                </conditional>
-            </conditional>
-            <output name="table" >
-                <assert_contents>
-                    <has_n_columns n="8" />
-                    <!-- should give nonsense empty output -->
-                    <has_line_matching expression="^\sc1\sc2\sc3\sg1\sg2\sg3\sg4$" />
-                    <has_line_matching expression="^g4\s+$" />
-                </assert_contents>
-            </output>
-        </test>
-        <test expect_num_outputs="1" >
-            <!-- Test 34: Subtracting table means #2 -->
-            <conditional name="singtabop" >
-                <param name="use_type" value="single" />
-                <param name="input" value="examples.5.tsv" />
-                <param name="col_row_names" value="has_col_names,has_row_names" />
-                <conditional name="user" >
-                    <param name="mode" value="fulltable" />
-                    <conditional name="general" >
-                        <param name="use" value="custom" />
-                        <param name="fulltable_custom_expr" value="table.sub(table.mean(1), 0).div(table.std(1),0)" />
-                    </conditional>
-                </conditional>
-            </conditional>
-            <output name="table" >
-                <assert_contents>
-                    <has_n_columns n="4" />
-                    <has_line_matching expression="^g1\s+-1\.\d+\s+0\.\d+\s+1\.\d+\s*$" />
-                    <has_line_matching expression="^g4\s+1\.1\d+\s+-0\.5\d+\s+-0\.5\d+\s*$" />
-                </assert_contents>
-            </output>
-        </test>
-        <test expect_num_outputs="1" >
-            <!-- Test 35: Subtracting table means #3 -->
-            <conditional name="singtabop" >
-                <param name="use_type" value="single" />
-                <param name="input" value="examples.5.tsv" />
-                <param name="col_row_names" value="has_col_names,has_row_names" />
-                <conditional name="user" >
-                    <param name="mode" value="fulltable" />
-                    <conditional name="general" >
-                        <param name="use" value="custom" />
-                        <param name="fulltable_custom_expr" value="(table.T - table.mean(1)).T" />
-                    </conditional>
-                </conditional>
-            </conditional>
-            <output name="table" >
-                <assert_contents>
-                    <has_n_columns n="4" />
-                    <has_line_matching expression="^g1\s+-10\.\d+\s+0\.\d+\s+10\.\d+\s*$" />
-                    <has_line_matching expression="^g4\s+47\.3\d+\s+-23\.6\d+\s+-23\.6\d+\s*$" />
-                </assert_contents>
-            </output>
-        </test>
-        <test expect_num_outputs="1" >
-            <!-- Test 36: Negative range test #1 -->
+            <!-- Test 34: Negative range test #1 -->
             <expand macro="test_inputs_ranges" >
                 <param name="select_cols_wanted" value="-2:2,1,-1" />
                 <param name="select_rows_wanted" value="1,3:-3,1" />
@@ -1154,7 +1116,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 37: Negative range test #2 -->
+            <!-- Test 35: Negative range test #2 -->
             <expand macro="test_inputs_ranges" >
                 <param name="select_cols_wanted" value="-1,-3,3:-3,2" />
                 <param name="select_rows_wanted" value="3:-1" />
@@ -1169,7 +1131,7 @@
             </output>
         </test>
         <test expect_num_outputs="1">
-            <!-- Test 38: Skip first 3 lines -->
+            <!-- Test 36: Skip first 3 lines -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="skiplines.tsv" />
@@ -1192,7 +1154,7 @@
             </output>
         </test>
         <test expect_num_outputs="1">
-            <!-- Test 39: Skip first 3 lines -->
+            <!-- Test 37: Skip first 3 lines -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="skiplines.tsv" />
@@ -1216,7 +1178,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 40: Row Col custom op #1 -->
+            <!-- Test 38: Row Col replace with format spec #1 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.1.tsv" />
@@ -1224,8 +1186,8 @@
                 <conditional name="user" >
                     <param name="mode" value="element" />
                     <conditional name="element" >
-                        <param name="mode" value="custom" />
-                        <param name="custom_expr" value="&#34;chr%.f&#34; % elem" />
+                        <param name="mode" value="replace" />
+                        <param name="replace_value" value="chr{elem:.0f}" />
                     </conditional>
                     <conditional name="elem_val" >
                         <param name="element_op" value="rowcol" />
@@ -1244,7 +1206,7 @@
             </output>
         </test>
         <test expect_num_outputs="1" >
-            <!-- Test 41: Row Col custom op #2 -->
+            <!-- Test 39: Row Col replace with format spec #2 -->
             <conditional name="singtabop" >
                 <param name="use_type" value="single" />
                 <param name="input" value="examples.1.tsv" />
@@ -1252,8 +1214,8 @@
                 <conditional name="user" >
                     <param name="mode" value="element" />
                     <conditional name="element" >
-                        <param name="mode" value="custom" />
-                        <param name="custom_expr" value="&#34;chr%.f&#34; % elem" />
+                        <param name="mode" value="replace" />
+                        <param name="replace_value" value="chr{elem:.0f}" />
                     </conditional>
                     <conditional name="elem_val" >
                         <param name="element_op" value="rowcol" />
@@ -1271,13 +1233,78 @@
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="1">
+            <!-- Test 40: Test safety of Replacement value free text
+            Tries to escape/reenter config file quoting.
+            If the test fails, this shows that Python has performed
+            string concatenation upon importing the config file. -->
+            <conditional name="singtabop" >
+                <param name="use_type" value="single" />
+                <param name="input" value="examples.1.tsv" />
+                <param name="col_row_names" value="has_col_names,has_row_names" />
+                <conditional name="user" >
+                    <param name="mode" value="element" />
+                    <conditional name="elem_val">
+                        <param name="element_op" value="None" />
+                    </conditional>
+                    <conditional name="element" >
+                        <param name="mode" value="replace" />
+                        <param name="scale_op" value="mod" />
+                        <param name="replace_value" value="a'+'b" />
+                    </conditional>
+                </conditional>
+            </conditional>
+            <output name="table" >
+                <assert_contents>
+                    <has_n_columns n="4" />
+                    <not_has_text text="g1&#009;ab" />
+                    <not_has_text text="g2&#009;ab" />
+                    <not_has_text text="g3&#009;ab" />
+                    <not_has_text text="g4&#009;ab" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1" expect_failure="true">
+            <!-- Test 41: Test safety of custom expression free text
+            Tries to escape/reenter config file quoting.
+
+            This test is expected to fail if either
+            - a validator disallows the use of single quotes or
+            - the single quotes get sanitized (which is unlikely to result in a
+              valid expression); note that in this situation, it cannot be
+              guaranteed that the single quote sanitization is safe with
+              *every* input
+
+            If the test succeeds unexpectedly, this shows that Python
+            has performed string concatenation upon importing the config file
+            resulting in each element of the test table being retained.
+             -->
+            <conditional name="singtabop" >
+                <param name="use_type" value="single" />
+                <param name="input" value="examples.4.tsv" />
+                <param name="col_row_names" value="has_col_names,has_row_names" />
+                <conditional name="user" >
+                    <param name="mode" value="element" />
+                    <conditional name="element" >
+                        <param name="mode" value="custom" />
+                        <param name="custom_expr" value="el'+'em" />
+                    </conditional>
+                    <conditional name="elem_val" >
+                        <param name="element_op" value="All" />
+                    </conditional>
+                </conditional>
+            </conditional>
+        </test>
     </tests>
     <help><![CDATA[
 This tool computes table expressions on the element, row, and column basis. It can sub-select,
 duplicate, as well as perform general and custom expressions on rows, columns or elements.
 
-Only a single operation can be performed on the data. Multiple operations can be performed by
-chaining successive runs of this tool. This is to provide a more transparent workflow for complex operations.
+.. class:: infomark
+
+    Only a single operation can be performed on the data. Multiple operations
+    can be performed by chaining successive runs of this tool. This is to
+    provide a more transparent workflow for complex operations.
 
 
 
@@ -1582,6 +1609,14 @@
 
     table1 / min(np.max(np.max(table2)), np.max(np.max(table3)))
 
+.. class:: infomark
+
+   Complex operations (like ones that would benefit from specifying nested
+   attributes) can often be broken into subsequent runs ot the tool, in
+   which the first run generates an intermediate table representing the result
+   of the "inner" operation that the second run can then use as input to
+   perform the "outer" operation.
+
 Also note that, currently `min()`, `max()` and `sum()` are the only built-in
 Python functions that can be used inside expressions. If you want to use
 additional functions, these have to be qualified functions from the `math`,
@@ -1702,11 +1737,17 @@
 
  * *Type of table operation* →  **Manipulate selected table elements**
 
-   * *Operation to perform* → **Custom**
+   * *Operation to perform* → **Replace values**
+
+     * *Replacement value* → ::
+
+         chr{elem:.0f}
 
-     * *Custom Expression* → ::
-
-         "chr%.f" % elem
+       Here, the placeholder ``{elem}`` lets us refer to each element's
+       current value, while the ``:.0f`` part is a format specifier that makes
+       sure numbers are printed without decimals (for a complete description of
+       the available syntax see the
+       `Python Format Specification Mini-Language <https://docs.python.org/3/library/string.html#formatspec>`_).
 
      * *Operate on elements* → **Specific Rows and/or Columns**
      * *List of columns to select* → "2"