diff table_compute.xml @ 3:60ff16842fcd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8"

--- a/table_compute.xml	Fri Sep 13 14:54:41 2019 -0400
+++ b/table_compute.xml	Fri Oct 18 06:22:51 2019 -0400
@@ -1297,8 +1297,14 @@
         </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.
+Table Compute
+-------------
+
+This tool is a Galaxy wrapper for the `Pandas Data Analysis Library <https://pandas.pydata.org/>`_ in Python,
+for manipulating and computing expressions upon tabular data and matrices. It can perform functions on the
+element, row, and column basis, as well as sub-select, duplicate, replace, and perform general and custom
+expressions on rows, columns, and elements.
+
 
 .. class:: infomark
 
@@ -1307,6 +1313,12 @@
     provide a more transparent workflow for complex operations.
 
 
+Many of the examples given below relate to common research use-cases such as filtering large matrices for
+specific values, counting unique instances of elements, conditionally manipulating the data, and replacing
+unwanted values. Full table operations such as normalisation can be easily performed by scaling the data via
+mean/median/min/max (and many other) metrics, and general expressions can even be computed across multiple
+tables.
+
 
 Examples
 ========
@@ -1325,7 +1337,8 @@
  g4  81   6   3
  === === === ===
 
-and we want to duplicate c1 and remove c2. Also select g1 to g3 and add g2 at the end as well. This would result in the output table:
+and we want to duplicate c1 and remove c2. Also select g1 to g3 and add g2 at the end as well. This
+ would result in the output table:
 
  === === === ===
   .  c1  c1  c3
@@ -1341,10 +1354,10 @@
  * *Input Single or Multiple Tables* → **Single Table**
  * *Column names on first row?* → **Yes**
  * *Row names on first column?* → **Yes**
- * *Type of table operation* →    **Drop, keep or duplicate rows and columns**
+ * *Type of table operation* → **Drop, keep or duplicate rows and columns**
 
-   * *List of columns to select* → **1,1,3**
-   * *List of rows to select* → **1:3,2**
+   * *List of columns to select* → ``1,1,3``
+   * *List of rows to select* → ``1:3,2``
    * *Keep duplicate columns* → **Yes**
    * *Keep duplicate rows* → **Yes**
 
@@ -1376,14 +1389,14 @@
  * *Input Single or Multiple Tables* → **Single Table**
  * *Column names on first row?* → **Yes**
  * *Row names on first column?* → **Yes**
- * *Type of table operation* →    **Filter rows or columns by their properties**
+ * *Type of table operation* → **Filter rows or columns by their properties**
 
    * *Filter* → **Rows**
    * *Filter Criterion* → **Result of function applied to columns/rows**
 
      * *Keep column/row if its observed* → **Sum**
      * *is* → **< (Less Than)**
-     * *this value* → **50**
+     * *this value* → ``50``
 
 
 Example 3: Count the number of values per row smaller than a specified value
@@ -1417,15 +1430,16 @@
  * *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**
+ * *Type of table operation* → **Manipulate selected table elements**
 
    * *Operation to perform* → **Custom**
 
-     * *Custom Expression on 'elem'* → **elem < 10**
+     * *Custom Expression on 'elem'* → ``elem < 10``
 
    * *Operate on elements* → **All**
 
-**Note:** *There are actually simpler ways to achieve our purpose, but here we are demonstrating the use of a custom expression.*
+**Note:** *There are actually simpler ways to achieve our purpose, but here we are demonstrating
+the use of a custom expression.*
 
 After executing, we would then be presented with a table like so:
 
@@ -1443,18 +1457,20 @@
  * *Input Single or Multiple Tables* → **Single Table**
  * *Column names on first row?* → **Yes**
  * *Row names on first column?* → **Yes**
- * *Type of table operation* →    **Compute Expression across Rows or Columns**
+ * *Type of table operation* → **Compute Expression across Rows or Columns**
 
    * *Calculate* → **Sum**
    * *For each* → **Row**
 
-Executing this will sum all the 'True' values in each row. Note that the values must have no extra whitespace in them for this to work (e.g. 'True ' or ' True' will not be parsed correctly).
+Executing this will sum all the 'True' values in each row. Note that the values must have no
+extra whitespace in them for this to work (e.g. 'True ' or ' True' will not be parsed correctly).
 
 
 Example 4: Perform a scaled log-transformation conditionally
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-We want to perform a scaled log transformation on all values greater than 5, and set all other values to 1.
+We want to perform a scaled log transformation on all values greater than 5, and set all
+other values to 1.
 
 We have the following table:
 
@@ -1483,13 +1499,11 @@
  * *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**
+ * *Type of table operation* → **Manipulate selected table elements**
 
    * *Operation to perform* → **Custom**
 
-     * *Custom Expression* → ::
-
-         (math.log(elem) / elem) if (elem > 5) else 1
+     * *Custom Expression* → ``(math.log(elem) / elem) if (elem > 5) else 1``
 
      * *Operate on elements* → **All**
 
@@ -1508,7 +1522,8 @@
  g4  81  10  10
  === === === ===
 
-and we want to subtract from each column the mean of that column divided by the standard deviation of it to yield:
+and we want to subtract from each column the mean of that column divided by the standard
+ deviation of it to yield:
 
 
  === ========= ========= =========
@@ -1528,10 +1543,7 @@
  * *Type of table operation* →  **Perform a Full Table Operation**
 
    * *Operation* → **Custom**
-
-   * *Custom Expression on 'table' along axis (0 or 1)* → ::
-
-      table - table.mean(0)/table.std(0)
+   * *Custom Expression on 'table' along axis (0 or 1)* → ``table - table.mean(0)/table.std(0)``
 
 
 Example 6: Perform operations on multiple tables
@@ -1658,8 +1670,8 @@
  * *Type of table operation* →  **Perform a Full Table Operation**
 
    * *Operation* → **Melt**
-   * *Variable IDs* → "A"
-   * *Unpivoted IDs* → "B,C"
+   * *Variable IDs* → ``A``
+   * *Unpivoted IDs* → ``B,C``
 
 This converts the "B" and "C" columns into variables.
 
@@ -1697,11 +1709,12 @@
  * *Type of table operation* →  **Perform a Full Table Operation**
 
    * *Operation* → **Pivot**
-   * *Index* → "foo"
-   * *Column* → "bar"
-   * *Values* → "baz"
+   * *Index* → ``foo``
+   * *Column* → ``bar``
+   * *Values* → ``baz``
 
-This splits the matrix using "foo" and "bar" using only the values from "baz". Header values may contain extra information.
+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
@@ -1739,23 +1752,21 @@
 
    * *Operation to perform* → **Replace values**
 
-     * *Replacement value* → ::
-
-         chr{elem:.0f}
+     * *Replacement value* → ``chr{elem:.0f}``
 
-       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
+       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"
-     * *List of rows to select* → "2,4"
-     * *Inclusive Selection* → "No"
+     * *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:
+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
@@ -1766,8 +1777,6 @@
  g4  chr81   chr6  chr3
  === =====  ===== =====
 
-
-
 ]]></help>
     <citations></citations>
 </tool>