# HG changeset patch
# User iuc
# Date 1567157298 14400
# Node ID dddadbbac949df48c789ad3100194d707b2d43ba
# Parent  1b0f96ed73f20919dd6ecc73f4101efa5f7b6f01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"

diff -r 1b0f96ed73f2 -r dddadbbac949 scripts/safety.py
--- a/scripts/safety.py	Sat Aug 17 16:25:37 2019 -0400
+++ b/scripts/safety.py	Fri Aug 30 05:28:18 2019 -0400
@@ -11,6 +11,7 @@
         '(', ')', 'if', 'else', 'or', 'and', 'not', 'in',
         '+', '-', '*', '/', '%', ',', '!=', '==', '>', '>=', '<', '<=',
         'min', 'max', 'sum',
+        'str', 'int', 'float'
     )
     __allowed_ref_types = {
         'pd.DataFrame': {
@@ -163,26 +164,25 @@
 
         safe = True
         # examples of user-expressions
-        # '-math.log(1 - elem/4096) * 4096 if elem != bn else elem - 0.5'
+        # '-math.log(1 - elem/4096) * 4096 if elem != 1 else elem - 0.5'
         # 'vec.median() +  vec.sum()'
 
         # 1. Break expressions into tokens
         # e.g.,
         # [
         #     '-', 'math.log', '(', '1', '-', 'elem', '/', '4096', ')', '*',
-        #     '4096', 'if', 'elem', '!=', 'bn', 'else', 'elem', '-', '0.5'
+        #     '4096', 'if', 'elem', '!=', '1', 'else', 'elem', '-', '0.5'
         # ]
         # or
         # ['vec.median', '(', ')', '+', 'vec.sum', '(', ')']
         tokens = [
             e for e in re.split(
-                r'([a-zA-Z0-9_.]+|[^a-zA-Z0-9_.() ]+|[()])', self.expr
+                r'("[a-zA-Z%0-9_.]+"|[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 = []
@@ -194,18 +194,32 @@
             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)
 
-        # 4. Assert that rest are real numbers
+        # 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:
-                safe = False
-                break
+                # e.g. '"TEXT"' is okay.
+                if not(e[0] == '"' and e[-1] == '"'):
+                    safe = False
+                    break
 
         return safe, e
diff -r 1b0f96ed73f2 -r dddadbbac949 scripts/table_compute.py
--- a/scripts/table_compute.py	Sat Aug 17 16:25:37 2019 -0400
+++ b/scripts/table_compute.py	Fri Aug 30 05:28:18 2019 -0400
@@ -3,7 +3,8 @@
 Table Compute tool - a wrapper around pandas with parameter input validation.
 """
 
-__version__ = "0.8"
+
+__version__ = "0.9.1"
 
 import csv
 import math
@@ -11,15 +12,17 @@
 
 import numpy as np
 import pandas as pd
-import userconfig as uc
 from safety import Safety
-# This should be generated in the same directory
 
-# Version command should not need to copy the config
 if len(argv) == 2 and argv[1] == "--version":
     print(__version__)
     exit(-1)
 
+# The import below should be generated in the same directory as
+# the table_compute.py script.
+# It is placed here so that the --version switch does not fail
+import userconfig as uc  # noqa: I100,I202
+
 
 class Utils:
     @staticmethod
@@ -37,12 +40,74 @@
         "Returns a valid two value DataFrame or Series operator"
         return getattr(type(pd_obj), "__" + op_name + "__")
 
+    @staticmethod
+    def readcsv(filedict, narm):
+        data = pd.read_csv(
+            filedict["file"],
+            header=filedict["header"],
+            index_col=filedict["row_names"],
+            keep_default_na=narm,
+            nrows=filedict["nrows"],
+            skipfooter=filedict["skipfooter"],
+            skip_blank_lines=filedict["skip_blank_lines"],
+            sep='\t'
+        )
+        # Fix whitespace issues in index or column names
+        data.columns = [col.strip() if type(col) is str else col
+                        for col in data.columns]
+        data.index = [row.strip() if type(row) is str else row
+                      for row in data.index]
+        return(data)
 
-# Math is imported but not directly used because users
-# may specify a "math.<function>" when inserting a custom
-# function. To remove linting errors, which break CI testing
-# we will just use an arbitrary math statement here.
-__ = math.log
+    @staticmethod
+    def rangemaker(tab):
+        # e.g. "1:3,2:-2" specifies "1,2,3,2,1,0,-1,-2" to give [0,1,2,1,0,-1,-2]
+        # Positive indices are decremented by 1 to reference 0-base numbering
+        # Negative indices are unaltered, so that -1 refers to the last column
+        out = []
+        err_mess = None
+        for ranges in tab.split(","):
+            nums = ranges.split(":")
+            if len(nums) == 1:
+                numb = int(nums[0])
+                # Positive numbers get decremented.
+                # i.e. column "3" refers to index 2
+                #      column "-1" still refers to index -1
+                if numb != 0:
+                    out.append(numb if (numb < 0) else (numb - 1))
+                else:
+                    err_mess = "Please do not use 0 as an index"
+            elif len(nums) == 2:
+                left, right = map(int, nums)
+                if 0 in (left, right):
+                    err_mess = "Please do not use 0 as an index"
+                elif left < right:
+                    if left > 0:  # and right > 0 too
+                        # 1:3 to 0,1,2
+                        out.extend(range(left - 1, right))
+                    elif right < 0:  # and left < 0 too
+                        # -3:-1 to -3,-2,-1
+                        out.extend(range(left, right + 1))
+                    elif left < 0 and right > 0:
+                        # -2:2 to -2,-1,0,1
+                        out.extend(range(left, 0))
+                        out.extend(range(0, right))
+                elif right < left:
+                    if right > 0:  # and left > 0
+                        # 3:1 to 2,1,0
+                        out.extend(range(left - 1, right - 2, -1))
+                    elif left < 0:  # and right < 0
+                        # -1:-3 to -1,-2,-3
+                        out.extend(range(left, right - 1, -1))
+                    elif right < 0 and left > 0:
+                        # 2:-2 to 1,0,-1,-2
+                        out.extend(range(left - 1, right - 1, -1))
+                else:
+                    err_mess = "%s should not be equal or contain a zero" % nums
+            if err_mess:
+                print(err_mess)
+                return(None)
+        return(out)
 
 
 # Set decimal precision
@@ -55,19 +120,7 @@
 
 if user_mode == "single":
     # Read in TSV file
-    data = pd.read_csv(
-        uc.Data["tables"][0]["reader_file"],
-        header=uc.Data["tables"][0]["reader_header"],
-        index_col=uc.Data["tables"][0]["reader_row_col"],
-        keep_default_na=uc.Default["narm"],
-        sep='\t'
-    )
-    # Fix whitespace issues in index or column names
-    data.columns = [col.strip() if type(col) is str else col
-                    for col in data.columns]
-    data.index = [row.strip() if type(row) is str else row
-                  for row in data.index]
-
+    data = Utils.readcsv(uc.Data["tables"][0], uc.Default["narm"])
     user_mode_single = params["user_mode_single"]
 
     if user_mode_single == "precision":
@@ -79,9 +132,13 @@
         rows_specified = params["select_rows_wanted"]
 
         # Select all indexes if empty array of values
-        if not cols_specified:
+        if cols_specified:
+            cols_specified = Utils.rangemaker(cols_specified)
+        else:
             cols_specified = range(len(data.columns))
-        if not rows_specified:
+        if rows_specified:
+            rows_specified = Utils.rangemaker(rows_specified)
+        else:
             rows_specified = range(len(data))
 
         # do not use duplicate indexes
@@ -161,16 +218,44 @@
     elif user_mode_single == "element":
         # lt, gt, ge, etc.
         operation = params["element_op"]
+        bool_mat = None
         if operation is not None:
-            op = Utils.getTwoValuePandaOp(operation, data)
-            value = params["element_value"]
-            try:
-                # Could be numeric
-                value = float(value)
-            except ValueError:
-                pass
-            # generate filter matrix of True/False values
-            bool_mat = op(data, value)
+            if operation == "rowcol":
+                # Select all indexes if empty array of values
+                if "element_cols" in params:
+                    cols_specified = Utils.rangemaker(params["element_cols"])
+                else:
+                    cols_specified = range(len(data.columns))
+                if "element_rows" in params:
+                    rows_specified = Utils.rangemaker(params["element_rows"])
+                else:
+                    rows_specified = range(len(data))
+
+                # Inclusive selection:
+                # - True: Giving a row or column will match all elements in that row or column
+                # - False: Give a row or column will match only elements in both those rows or columns
+                inclusive = params["element_inclusive"]
+
+                # Create a bool matrix (intialised to False) with selected
+                # rows and columns set to True
+                bool_mat = data.copy()
+                bool_mat[:] = False
+                if inclusive:
+                    bool_mat.iloc[rows_specified, :] = True
+                    bool_mat.iloc[:, cols_specified] = True
+                else:
+                    bool_mat.iloc[rows_specified, cols_specified] = True
+
+            else:
+                op = Utils.getTwoValuePandaOp(operation, data)
+                value = params["element_value"]
+                try:
+                    # Could be numeric
+                    value = float(value)
+                except ValueError:
+                    pass
+                # generate filter matrix of True/False values
+                bool_mat = op(data, value)
         else:
             # implement no filtering through a filter matrix filled with
             # True values.
@@ -265,13 +350,7 @@
 
     # Read and populate tables
     for x, t_sect in enumerate(table_sections):
-        tmp = pd.read_csv(
-            t_sect["file"],
-            header=t_sect["header"],
-            index_col=t_sect["row_names"],
-            keep_default_na=uc.Default["narm"],
-            sep="\t"
-        )
+        tmp = Utils.readcsv(t_sect, uc.Default["narm"])
         table.append(tmp)
         table_names.append("table" + str(x + 1))
         table_names_real.append("table[" + str(x) + "]")
diff -r 1b0f96ed73f2 -r dddadbbac949 table_compute.xml
--- a/table_compute.xml	Sat Aug 17 16:25:37 2019 -0400
+++ b/table_compute.xml	Fri Aug 30 05:28:18 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@">0.8</token>
+        <token name="@VERSION@">0.9.1</token>
         <token name="@COPEN@"><![CDATA[<code>]]></token>
         <token name="@CCLOSE@"><![CDATA[</code>]]></token>
         <import>allowed_functions.xml</import>
@@ -19,11 +19,11 @@
             <sanitizer sanitize="false" />
         </macro>
         <macro name="validator_index_ranges">
-            <validator type="regex" message="Specify a comma-separated list index numbers or ranges">^(?:\d+(?::\d)*(?:, *\d+(?::\d)*)*)?$</validator>
+            <validator type="regex" message="Specify a comma-separated list index numbers or ranges">^(?:-?\d+(?::-?\d+)*(?:, *-?\d+(?::-?\d+)*)*)?$</validator>
             <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 -->
@@ -36,6 +36,16 @@
                 </conditional>
             </conditional>
         </macro>
+        <macro name="test_inputs_ranges" >
+            <conditional name="singtabop" >
+                <param name="use_type" value="single" />
+                <param name="input" value="examples.1.tsv" />
+                <conditional name="user" >
+                    <param name="mode" value="select" />
+                    <yield />
+                </conditional>
+            </conditional>
+        </macro>
         <!-- macro for umi to transcript tests -->
         <macro name="umi2trans" >
             <yield />
@@ -53,14 +63,31 @@
         <macro name="file_opts">
             <param name="input" type="data" format="tsv,tabular" label="Table" />
             <param name="col_row_names" type="select" display="checkboxes" multiple="true" optional="true"
-            label="This input data has">
+                   label="Input data has">
                 <option value="has_col_names" selected="true">Column names on the first row</option>
-                <option value="has_row_names" selected="true">Row names on the first column"</option>
+                <option value="has_row_names" selected="true">Row names on the first column</option>
             </param>
+            <section name="adv" title="Advanced File Options " expanded="false" >
+                <param name="header" type="integer" min="0" optional="true" label="Header begins at line N" help="All lines before line N will be skipped. If a value is set, this will override the above 'Column names on the first row' parameter." />
+                <param name="nrows" type="integer" min="0" optional="true" label="Read N lines only" help="Parses only N lines after the header line." />
+                <param name="skipfooter" type="integer" min="0" optional="true" label="Skip N lines from bottom" help="Do not use this in conjunction with the 'Read N lines only' parameter." />
+                <param name="skip_blank_lines" type="boolean" checked="true" falsevalue="False" truevalue="True" label="Skip blank lines" help="Otherwise it will insert NaN values for every blank line detected." />
+            </section>
         </macro>
         <!-- element value macro -->
-        <macro name="elem_val_macro" >
-            <param name="element_value" type="text" optional="true" label="Filter value" help="This value is converted to numeric if possible, otherwise it is treated as a string" />
+        <macro name="elem_val_macro" token_when="@WHEN@" >
+            <when value="@WHEN@" >
+                <param name="element_value" type="text" optional="true" label="Filter value" help="This value is converted to numeric if possible, otherwise it is treated as a string" />
+            </when>
+        </macro>
+        <!-- Row/Col macro -->
+        <macro name="select_rowcols" >
+            <param name="select_cols_wanted" type="text" optional="true" label="List of columns to select" help="Comma separated. (e.g. @COPEN@3:5,10,-1,2:-2@CCLOSE@ will select columns @COPEN@3,4,5,10,-1,2,1,0,-1,-2@CCLOSE@, where negative indices refer to the offset from the last index). Columns can be duplicated by specifying them multiple times. Leave blank to retain all columns. See Example #1 for an example of using this mode." >
+                <expand macro="validator_index_ranges" />
+            </param>
+            <param name="select_rows_wanted" type="text" optional="true" label="List of rows to select" help="The same rules apply as above" >
+                <expand macro="validator_index_ranges" />
+            </param>
         </macro>
     </macros>
     <requirements>
@@ -69,7 +96,7 @@
     </requirements>
 
     <version_command><![CDATA[
-        touch '$__tool_directory__/scripts/userconfig.py' && python '$__tool_directory__/scripts/table_compute.py' --version
+        python '$__tool_directory__/scripts/table_compute.py' --version
     ]]></version_command>
 
     <command detect_errors="exit_code"><![CDATA[
@@ -83,15 +110,6 @@
     ]]></command>
     <configfiles>
         <configfile name="userconf"><![CDATA[
-
-## Range Maker
-##  "2:5,11,1:2" specifies "2,3,4,5,11,1,2" which in python is "1,2,3,4,10,0,1"
-#def rangemake(tab):
-#echo    [(n-1) for r in map(lambda y: range(int(y[0]),int(y[-1])+1), map(lambda x: x.split(':'), tab.split(','))) for n in r]
-#end def
-
-## Strip leading and trailing whitespace off custom functions
-
 Default = {
     "reader_skip": 0,
     "precision": $precision,
@@ -118,16 +136,25 @@
 Data = {
     "tables": [
         {
-          "reader_file": '$singtabop.input',
-        #if 'has_col_names' in str($singtabop.col_row_names):
-          "reader_header": 0,
+          "file": '$singtabop.input',
+        #if $singtabop.adv.header:
+          "header": int('$singtabop.adv.header'),
+        #elif 'has_col_names' in str($singtabop.col_row_names):
+          "header": 0,
         #else:
-          "reader_header": None,
+          "header": None,
         #end if
-        #if 'has_row_names' in str($singtabop.col_row_names):
-          "reader_row_col": 0,
-        #else:
-          "reader_row_col": False,
+          "row_names": #if ('has_row_names' in str($singtabop.col_row_names)) then 0 else False#,
+          "skipfooter": #if $singtabop.adv.skipfooter then int($singtabop.adv.skipfooter) else 0#,
+        #if $singtabop.adv.skip_blank_lines
+          "skip_blank_lines": $singtabop.adv.skip_blank_lines,
+        #else
+          "skip_blank_lines": None,
+        #end if
+        #if $singtabop.adv.nrows
+          "nrows": int('$singtabop.adv.nrows'),
+        #else
+          "nrows": None,
         #end if
         }
     ],
@@ -141,12 +168,12 @@
         "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:
-        "select_cols_wanted": $rangemake(str($singtabop.user.select_cols_wanted)),
+        "select_cols_wanted": '$singtabop.user.select_cols_wanted',
       #else
         "select_cols_wanted": None,
       #end if
       #if $singtabop.user.select_rows_wanted:
-        "select_rows_wanted": $rangemake(str($singtabop.user.select_rows_wanted)),
+        "select_rows_wanted": '$singtabop.user.select_rows_wanted',
       #else
         "select_rows_wanted": None,
       #end if
@@ -181,12 +208,21 @@
       #end if
     }
     #elif $singtabop.user.mode.value == 'element':
-      #if str($singtabop.user.elem_val.element_op) != "None":
+      #if str($singtabop.user.elem_val.element_op) == "None":
+        "element_op": None,
+      #elif str($singtabop.user.elem_val.element_op) == "rowcol":
+        "element_op": "rowcol",
+          #if $singtabop.user.elem_val.select_rows_wanted
+        "element_rows": '$singtabop.user.elem_val.select_rows_wanted',
+          #end if
+          #if $singtabop.user.elem_val.select_cols_wanted
+        "element_cols": '$singtabop.user.elem_val.select_cols_wanted',
+          #end if
+        "element_inclusive": $singtabop.user.elem_val.inclusive_selection,
+      #else:
         "element_op": '$singtabop.user.elem_val.element_op.value',
         ## Value is string or float, parsed in code later
         "element_value" : '$singtabop.user.elem_val.element_value',
-      #else:
-        "element_op": None,
       #end if
         "element_mode": '$singtabop.user.element.mode.value',
       #if str($singtabop.user.element.mode) == "replace":
@@ -252,16 +288,26 @@
     #for $i, $s in enumerate($singtabop.tables)
         {
           "file": '${s.input}',
-        #if 'has_col_names' in str($s.col_row_names):
+        #if $s.adv.header:
+          "header": int('${s.adv.header}'),
+        #elif 'has_col_names' in str($s.col_row_names):
           "header": 0,
         #else:
           "header": None,
         #end if
-        #if 'has_row_names' in str($s.col_row_names):
-          "row_names": 0,
-        #else:
-          "row_names": False,
+          "row_names": #if ('has_row_names' in str($s.col_row_names)) then 0 else False#,
+          "skipfooter": #if $s.adv.skipfooter then int('$s.adv.skipfooter') else 0#,
+        #if $s.adv.skip_blank_lines:
+          "skip_blank_lines": $s.adv.skip_blank_lines,
+        #else
+           "skip_blank_lines": None,
         #end if
+        #if $s.adv.nrows:
+           "nrows": int('${s.adv.nrows}'),
+        #else
+           "nrows": None,
+        #end if
+
         },
     #end for
     ],
@@ -293,12 +339,7 @@
                     </param>
                     <when value="precision" />
                     <when value="select">
-                        <param name="select_cols_wanted" type="text" optional="true" label="List of columns to select" help="Comma separated. (e.g. @COPEN@3:5,99,2:4@CCLOSE@ will select columns @COPEN@3,4,5,99,2,3,4@CCLOSE@). Columns can be duplicated by specifying them multiple times. Leave blank to retain all columns. See Example #1 for an example of using this mode." >
-                            <expand macro="validator_index_ranges" />
-                        </param>
-                        <param name="select_rows_wanted" type="text" optional="true" label="List of rows to select" help="The same rules apply as above" >
-                            <expand macro="validator_index_ranges" />
-                        </param>
+                        <expand macro="select_rowcols" />
                         <param name="select_keepdupe" type="select" display="checkboxes" multiple="true" label="Duplicate Indices" help="Keep duplicates when specifying ranges (e.g. if unset, @COPEN@1:3,2:4@CCLOSE@ will yield @COPEN@1,2,3,4@CCLOSE@ instead of @COPEN@1,2,3,2,3,4@CCLOSE@)" >
                             <option value="select_cols_keepdupe" selected="true" >Keep duplicate columns</option>
                             <option value="select_rows_keepdupe" selected="true" >Keep duplicate rows</option>
@@ -447,38 +488,30 @@
                                 <param name="scale_value" type="float" value="0" label="Second operand value" />
                             </when>
                             <when value="custom">
-                                <param name="custom_expr" type="text"
-                                label="Custom expression on 'elem'"
-                                help="The parameter name is @COPEN@elem@CCLOSE@, referring to the element being acted on. Most operators and @COPEN@if@CCLOSE@ @COPEN@else@CCLOSE@ statements are supported. See Examples #3 and #4 in the Help section.">
+                                <param name="custom_expr" type="text" label="Custom expression on 'elem'"
+                                       help="The parameter name is @COPEN@elem@CCLOSE@, referring to the element being acted on. Most operators and @COPEN@if@CCLOSE@ @COPEN@else@CCLOSE@ statements are supported. See Examples #3 and #4 in the Help section.">
                                     <expand macro="validator_functiondef" />
                                 </param>
                             </when>
                         </conditional>
                         <conditional name="elem_val" >
                             <param name="element_op" type="select" label="Operate on elements"
-                                help="Only selected elements will be manipulated. Other elements will retain their original value." >
+                                   help="Only selected elements will be manipulated. Other elements will retain their original value." >
                                 <expand macro="select_twovaluebooleanops" >
                                     <option value="None" selected="true">All</option>
+                                    <option value="rowcol" >Specific Rows and/or Columns</option>
                                 </expand>
                             </param>
                             <when value="None" />
-                            <when value="lt">
-                                <expand macro="elem_val_macro" />
-                            </when>
-                            <when value="le">
-                                <expand macro="elem_val_macro" />
-                            </when>
-                            <when value="gt">
-                                <expand macro="elem_val_macro" />
-                            </when>
-                            <when value="ge">
-                                <expand macro="elem_val_macro" />
-                            </when>
-                            <when value="eq">
-                                <expand macro="elem_val_macro" />
-                            </when>
-                            <when value="ne">
-                                <expand macro="elem_val_macro" />
+                            <expand macro="elem_val_macro" when="lt" />
+                            <expand macro="elem_val_macro" when="le" />
+                            <expand macro="elem_val_macro" when="gt" />
+                            <expand macro="elem_val_macro" when="ge" />
+                            <expand macro="elem_val_macro" when="eq" />
+                            <expand macro="elem_val_macro" when="ne" />
+                            <when value="rowcol" >
+                                <expand macro="select_rowcols" />
+                                <param name="inclusive_selection" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Inclusive Selection" help="If enabled, all elements that match ANY row or column given above will be acted on. Otherwise, only the elements that match BOTH a row or column given above will be acted on." />
                             </when>
                         </conditional>
                     </when>
@@ -1039,6 +1072,205 @@
                 </assert_contents>
             </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 -->
+            <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" />
+            </expand>
+            <output name="table" >
+                <assert_contents>
+                    <has_n_columns n="7" />
+                    <has_line_matching expression="^\s*c2\s+c3\s+c1\s+c2\s+c1\s+c3$" />
+                    <has_line_matching expression="^g1\s+20\s+30\s+10\s+20\s+10\s+30$" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1" >
+            <!-- Test 37: 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" />
+                <param name="select_keepdupe" value="" />
+            </expand>
+            <output name="table" >
+                <assert_contents>
+                    <has_n_columns n="7" />
+                    <has_line_matching expression="^\s*c3\s+c1\s+c3\s+c2\s+c1\s+c2$" />
+                    <has_line_matching expression="^g4\s+3\s+81\s+3\s+6\s+81\s+6$" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- Test 38: Skip first 3 lines -->
+            <conditional name="singtabop" >
+                <param name="use_type" value="single" />
+                <param name="input" value="skiplines.tsv" />
+                <section name="adv" >
+                    <param name="header" value="2" />
+                    <param name="nrows" value="4" />
+                    <param name="skip_blank_lines" value="true" />
+                </section>
+                <conditional name="user" >
+                    <param name="mode" value="precision" />
+                </conditional>
+            </conditional>
+            <param name="precision" value="2" />
+            <output name="table" >
+                <assert_contents>
+                    <has_n_columns n="4" />
+                    <has_line_matching expression="^\s+c1\s+c2\s+c3$" />
+                    <has_line_matching expression="^g4\s+81\s+6\s+3$" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- Test 39: Skip first 3 lines -->
+            <conditional name="singtabop" >
+                <param name="use_type" value="single" />
+                <param name="input" value="skiplines.tsv" />
+                <section name="adv" >
+                    <param name="header" value="2" />
+                    <param name="skipfooter" value="2" />
+                    <param name="skip_blank_lines" value="false" />
+                </section>
+                <conditional name="user" >
+                    <param name="mode" value="precision" />
+                </conditional>
+            </conditional>
+            <param name="precision" value="2" />
+            <param name="out_opts" value="" />
+            <output name="table" >
+                <assert_contents>
+                    <has_n_columns n="3" />
+                    <has_line_matching expression="^10.00\s+20.00\s+30.00$" />
+                    <has_line_matching expression="^\s+$" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1" >
+            <!-- Test 40: Row Col custom op #1 -->
+            <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="element" >
+                        <param name="mode" value="custom" />
+                        <param name="custom_expr" value="&#34;chr%.f&#34; % elem" />
+                    </conditional>
+                    <conditional name="elem_val" >
+                        <param name="element_op" value="rowcol" />
+                        <param name="select_cols_wanted" value="2" />
+                        <param name="select_rows_wanted" value="2,4" />
+                        <param name="inclusive_selection" value="True" />
+                    </conditional>
+                </conditional>
+            </conditional>
+            <output name="table" >
+                <assert_contents>
+                    <has_n_columns n="4" />
+                    <has_line_matching expression="^g2\s+chr3\s+chr6\s+chr9$" />
+                    <has_line_matching expression="^g4\s+chr81\s+chr6\s+chr3$" />
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1" >
+            <!-- Test 41: Row Col custom op #2 -->
+            <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="element" >
+                        <param name="mode" value="custom" />
+                        <param name="custom_expr" value="&#34;chr%.f&#34; % elem" />
+                    </conditional>
+                    <conditional name="elem_val" >
+                        <param name="element_op" value="rowcol" />
+                        <param name="select_cols_wanted" value="2" />
+                        <param name="select_rows_wanted" value="2,4" />
+                        <param name="inclusive_selection" value="False" />
+                    </conditional>
+                </conditional>
+            </conditional>
+            <output name="table" >
+                <assert_contents>
+                    <has_n_columns n="4" />
+                    <has_line_matching expression="^g2\s+3\s+chr6\s+9$" />
+                    <has_line_matching expression="^g4\s+81\s+chr6\s+3$" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 This tool computes table expressions on the element, row, and column basis. It can sub-select,
@@ -1436,6 +1668,65 @@
 
 This splits the matrix using "foo" and "bar" using only the values from "baz". Header values may contain extra information.
 
+
+Example 9: Replacing text in specific rows or columns
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+We have the following table
+
+ === === === ===
+  .  c1  c2  c3
+ === === === ===
+ g1  10  20  30
+ g2   3   3   9
+ g3   4   8  12
+ g4  81   6   3
+ === === === ===
+
+and we want to add "chr" to the elements in column 2 AND rows 2 and 4:
+
+ === === ==== ===
+  .  c1    c2  c3
+ === === ==== ===
+ g1  10    20  30
+ g2   3  chr3   9
+ g3   4     8  12
+ g4  81  chr6   3
+ === === ==== ===
+
+In Galaxy we would select the following:
+
+ * *Input Single or Multiple Tables* → **Single Table**
+ * *Column names on first row?* → **Yes**
+ * *Row names on first column?* → **Yes**
+
+ * *Type of table operation* →  **Manipulate selected table elements**
+
+   * *Operation to perform* → **Custom**
+
+     * *Custom Expression* → ::
+
+         "chr%.f" % elem
+
+     * *Operate on elements* → **Specific Rows and/or Columns**
+     * *List of columns to select* → "2"
+     * *List of rows to select* → "2,4"
+     * *Inclusive Selection* → "No"
+
+
+If we wanted to instead add "chr" to the ALL elements in column 2 and rows 2 and 4, we would repeat the steps above but set the *Inclusive Selection* to "Yes", to give:
+
+ === =====  ===== =====
+  .    c1     c2    c3
+ === =====  ===== =====
+ g1     10  chr20    30
+ g2   chr3   chr3  chr9
+ g3      4      8    12
+ g4  chr81   chr6  chr3
+ === =====  ===== =====
+
+
+
 ]]></help>
     <citations></citations>
 </tool>
diff -r 1b0f96ed73f2 -r dddadbbac949 test-data/skiplines.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/skiplines.tsv	Fri Aug 30 05:28:18 2019 -0400
@@ -0,0 +1,10 @@
+A1	A6	A7	A8
+A2	A3	A4	A5
+	c1	c2	c3
+g1	10	20	30
+g2	3	6	9
+g3	4	8	12
+g4	81	6	3
+            
+A1	A6	A7	A8
+A2	A3	A4	A5
\ No newline at end of file