--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/awklike-mutate.xml	Tue May 19 17:15:08 2020 -0400
@@ -0,0 +1,178 @@
+<tool id="csvtk_awklike_mutate" name="csvtk-advanced-mutate" version="@VERSION@+@GALAXY_VERSION@">
+    <description> new column by awk-like artithmetic/string expressions</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_cmd" />
+    <command detect_errors="exit_code"><![CDATA[
+
+###################
+## Start Command ##
+###################
+csvtk mutate2 --num-cpus "\${GALAXY_SLOTS:-1}"
+
+    ## Add additional flags as specified ##
+    #######################################
+    $global_param.illegal_rows
+    $global_param.empty_rows
+    $global_param.header
+    $global_param.lazy_quotes
+
+    ## Set Tabular input/output flag if first input is tabular ##
+    #############################################################
+    #if $in_1.is_of_type("tabular"):
+        -t -T
+    #end if
+
+    ## Set input files ##
+    #####################
+    $in_1
+
+    ## Specific inputs ##
+    #####################
+    -e '$in_text'
+    -n '$column_name'
+    -L '$additional.digit_number'
+    $additional.digit_strings
+    
+    ## To output ##
+    ###############
+    > mutated
+
+    ]]></command>
+    <inputs>
+        <expand macro="singular_input"/>
+        <param name="in_text" type="text" argument="-e" label="Awk-like artithmetic/string expression" >
+            <help>
+                <![CDATA[
+        Examples:
+        - '$age>12'
+        - '$1 > $3'
+        - '$name=="abc"'
+        - '$1 % 2 == 0'
+        More info is available in the help section below. The ' character is invalid and will be replaced, thus you must
+        surround strings with double quotes ("string") instead.
+        ]]>
+            </help>
+            <expand macro="text_sanitizer" />
+        </param>
+        <param name="column_name" type="text" argument="-n" value="New_Column"
+            label="New column name"
+            help="Specify what the new column should be called">
+            <expand macro="text_sanitizer" />
+        </param>
+        <section name="additional" title="Additional Parameters" expanded="true">
+            <param name="digit_number" type="integer" value="2" argument="-L"
+                label="Number of digits after the decimal to keep"
+                help="Keep input integer number of decimal places"
+            />
+            <param name="digit_strings" type="boolean" checked="false" argument="-s"
+                truevalue="-s"
+                falsevalue=""
+                label="Input digits as strings"
+                help="Treat digits as string to avoid converting big digits into scientific notation. No longer supports mathematical operations if set to yes"
+            />
+        </section>
+        <expand macro="global_parameters" />
+    </inputs>
+    <outputs>
+        <data format_source="in_1" from_work_dir="mutated" name="mutated" label="${in_1.name} mutated by ${in_text}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_1" value="awk_mutate_input.csv" />
+            <param name="in_text" value="$2*$3" />
+            <param name="column_name" value="CFU/ml" />
+            <section name="additional">
+                <param name="digit_number" value="0" />
+            </section>
+            <output name="mutated" file="awk_mutate_output.csv" ftype="csv" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    
+Csvtk - Mutate2 Help
+--------------------
+
+Info
+####
+
+Csvtk advanced mutate (also called mutate2) outputs a column that evaluates the input expression. Please see the
+`documentation <https://github.com/Knetic/govaluate/blob/master/MANUAL.md>`_ for further details and examples on how to write expressions.
+
+Also checkout the tools `website <https://bioinf.shenwei.me/csvtk/usage/#mutate2>`_ for additional ideas on how to structure expressions!
+
+.. class:: warningmark
+
+    Single quotes are not allowed in text inputs!
+
+.. class:: note
+
+    If your wanted column header has a space in it, use the column number. Example: Use $1 if column #1 is called "Colony Counts"
+
+Supported operators and types:
+
+    - Modifiers: + - / * & | ^ ** % >> <<
+    - Comparators: > >= < <= == != =~ !~
+    - Logical ops: || &&
+    - Numeric constants, as 64-bit floating point (12345.678)
+    - String constants (double quotes only: "foobar")
+    - Date constants (double quotes)
+    - Boolean constants: true false
+    - Parenthesis to control order of evaluation ( )
+    - Arrays (anything separated by , within parenthesis: (1, 2, "foo"))
+    - Prefixes: ! - ~
+    - Ternary conditional: ? :
+    - Null coalescence: ??
+
+----
+
+@HELP_INPUT_DATA@
+
+
+Usage
+#####
+
+Some quick and simple examples:
+
+**Ex. Mutate2 with Numbers:**
+
+Suppose we had the following table:
+
++---------------+------------+----------+
+| Culture Label | Cell Count | Dilution |
++===============+============+==========+
+| ECo-1         | 2523       | 1000     |
++---------------+------------+----------+
+| LPn-1         | 100        | 1000000  |
++---------------+------------+----------+
+| LPn-2         | 4          | 1000     |
++---------------+------------+----------+
+
+If we wanted to evaluate the CFU/ml of these samples (supposing a 1ml volume plated) with this tool,
+we could create give our new column a name like "CFU/ml" and then use the expression "$2*$3" to get:
+
++---------------+------------+----------+-----------+
+| Culture Label | Cell Count | Dilution | CFU/ml    |
++===============+============+==========+===========+
+| ECo-1         | 2523       | 1000     | 2523000   |
++---------------+------------+----------+-----------+
+| LPn-1         | 100        | 1000000  | 100000000 |
++---------------+------------+----------+-----------+
+| LPn-2         | 4          | 1000     | 4000      |
++---------------+------------+----------+-----------+
+
+Note how $2 was used to get column 2 due to it containing a space in its name
+
+----
+
+@HELP_COLUMNS@
+
+
+@HELP_END_STATEMENT@
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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