table_compute: table_compute.xml comparison

comparison table_compute.xml @ 3:60ff16842fcd draft

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

author	iuc
date	Fri, 18 Oct 2019 06:22:51 -0400
parents	02c3e335a695
children	93a3ce78ce55

comparison

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 </conditional>
 </conditional>
 </test>
 </tests>
 <help><![CDATA[
-This tool computes table expressions on the element, row, and column basis. It can sub-select,
+Table Compute
-duplicate, as well as perform general and custom expressions on rows, columns or elements.
+-------------
+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
 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.
+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
 ========
 g2   3   6   9
 g3   4   8  12
 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
 === === === ===
 g1  10  10  30
 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* →    **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 columns to select* → ``1,1,3``
-* *List of rows to select* → **1:3,2**
+* *List of rows to select* → ``1:3,2``
 * *Keep duplicate columns* → **Yes**
 * *Keep duplicate rows* → **Yes**
 Example 2: Filter for rows with row sums less than 50
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 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* →    **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
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 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**
+* *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:
 === ===== ===== =====
 .     c1    c2    c3
 To get to our desired table, we would then process this table with the tool again:
 * *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:
 === === === ===
 .  c1  c2  c3
 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**
+* *Type of table operation* → **Manipulate selected table elements**
 * *Operation to perform* → **Custom**
-* *Custom Expression* → ::
+* *Custom Expression* → ``(math.log(elem) / elem) if (elem > 5) else 1``
-(math.log(elem) / elem) if (elem > 5) else 1
 * *Operate on elements* → **All**
 Example 5: Perform a Full table operation
 g2   3  10   9
 g3   4   8  10
 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:
 === ========= ========= =========
 .         c1        c2        c3
 === ========= ========= =========
 * *Column names on first row?* → **Yes**
 * *Row names on first column?* → **Yes**
 * *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
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 * *Column names on first row?* → **Yes**
 * *Row names on first column?* → **Yes**
 * *Type of table operation* →  **Perform a Full Table Operation**
 * *Operation* → **Melt**
-* *Variable IDs* → "A"
+* *Variable IDs* → ``A``
-* *Unpivoted IDs* → "B,C"
+* *Unpivoted IDs* → ``B,C``
 This converts the "B" and "C" columns into variables.
 Example 8: Pivot
 * *Column names on first row?* → **Yes**
 * *Row names on first column?* → **Yes**
 * *Type of table operation* →  **Perform a Full Table Operation**
 * *Operation* → **Pivot**
-* *Index* → "foo"
+* *Index* → ``foo``
-* *Column* → "bar"
+* *Column* → ``bar``
-* *Values* → "baz"
+* *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
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 * *Type of table operation* →  **Manipulate selected table elements**
 * *Operation to perform* → **Replace values**
-* *Replacement value* → ::
+* *Replacement value* → ``chr{elem:.0f}``
-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
-Here, the placeholder ``{elem}`` lets us refer to each element's
+without decimals (for a complete description of the available syntax see the
-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 columns to select* → ``2``
-* *List of rows to select* → "2,4"
+* *List of rows to select* → ``2,4``
-* *Inclusive Selection* → "No"
+* *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
 === =====  ===== =====
 g1     10  chr20    30
 g2   chr3   chr3  chr9
 g3      4      8    12
 g4  chr81   chr6  chr3
 === =====  ===== =====
 ]]></help>
 <citations></citations>
 </tool>

Mercurial > repos > iuc > table_compute

comparison table_compute.xml @ 3:60ff16842fcd draft