| Previous changeset 2:02c3e335a695 (2019-09-13) Next changeset 4:93a3ce78ce55 (2021-04-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 5c7c463baf40edda673a569e91b2c2a5e3b6b4f8" |
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modified:
table_compute.xml |
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| diff -r 02c3e335a695 -r 60ff16842fcd table_compute.xml --- a/table_compute.xml Fri Sep 13 14:54:41 2019 -0400 +++ b/table_compute.xml Fri Oct 18 06:22:51 2019 -0400 |
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| b"@@ -1297,8 +1297,14 @@\n </test>\n </tests>\n <help><![CDATA[\n-This tool computes table expressions on the element, row, and column basis. It can sub-select,\n-duplicate, as well as perform general and custom expressions on rows, columns or elements.\n+Table Compute\n+-------------\n+\n+This tool is a Galaxy wrapper for the `Pandas Data Analysis Library <https://pandas.pydata.org/>`_ in Python,\n+for manipulating and computing expressions upon tabular data and matrices. It can perform functions on the\n+element, row, and column basis, as well as sub-select, duplicate, replace, and perform general and custom\n+expressions on rows, columns, and elements.\n+\n \n .. class:: infomark\n \n@@ -1307,6 +1313,12 @@\n provide a more transparent workflow for complex operations.\n \n \n+Many of the examples given below relate to common research use-cases such as filtering large matrices for\n+specific values, counting unique instances of elements, conditionally manipulating the data, and replacing\n+unwanted values. Full table operations such as normalisation can be easily performed by scaling the data via\n+mean/median/min/max (and many other) metrics, and general expressions can even be computed across multiple\n+tables.\n+\n \n Examples\n ========\n@@ -1325,7 +1337,8 @@\n g4 81 6 3\n === === === ===\n \n-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:\n+and we want to duplicate c1 and remove c2. Also select g1 to g3 and add g2 at the end as well. This\n+ would result in the output table:\n \n === === === ===\n . c1 c1 c3\n@@ -1341,10 +1354,10 @@\n * *Input Single or Multiple Tables* \xe2\x86\x92 **Single Table**\n * *Column names on first row?* \xe2\x86\x92 **Yes**\n * *Row names on first column?* \xe2\x86\x92 **Yes**\n- * *Type of table operation* \xe2\x86\x92 **Drop, keep or duplicate rows and columns**\n+ * *Type of table operation* \xe2\x86\x92 **Drop, keep or duplicate rows and columns**\n \n- * *List of columns to select* \xe2\x86\x92 **1,1,3**\n- * *List of rows to select* \xe2\x86\x92 **1:3,2**\n+ * *List of columns to select* \xe2\x86\x92 ``1,1,3``\n+ * *List of rows to select* \xe2\x86\x92 ``1:3,2``\n * *Keep duplicate columns* \xe2\x86\x92 **Yes**\n * *Keep duplicate rows* \xe2\x86\x92 **Yes**\n \n@@ -1376,14 +1389,14 @@\n * *Input Single or Multiple Tables* \xe2\x86\x92 **Single Table**\n * *Column names on first row?* \xe2\x86\x92 **Yes**\n * *Row names on first column?* \xe2\x86\x92 **Yes**\n- * *Type of table operation* \xe2\x86\x92 **Filter rows or columns by their properties**\n+ * *Type of table operation* \xe2\x86\x92 **Filter rows or columns by their properties**\n \n * *Filter* \xe2\x86\x92 **Rows**\n * *Filter Criterion* \xe2\x86\x92 **Result of function applied to columns/rows**\n \n * *Keep column/row if its observed* \xe2\x86\x92 **Sum**\n * *is* \xe2\x86\x92 **< (Less Than)**\n- * *this value* \xe2\x86\x92 **50**\n+ * *this value* \xe2\x86\x92 ``50``\n \n \n Example 3: Count the number of values per row smaller than a specified value\n@@ -1417,15 +1430,16 @@\n * *Input Single or Multiple Tables* \xe2\x86\x92 **Single Table**\n * *Column names on first row?* \xe2\x86\x92 **Yes**\n * *Row names on first column?* \xe2\x86\x92 **Yes**\n- * *Type of table operation* \xe2\x86\x92 **Manipulate selected table elements**\n+ * *Type of table operation* \xe2\x86\x92 **Manipulate selected table elements**\n \n * *Operation to perform* \xe2\x86\x92 **Custom**\n \n- * *Custom Expression on 'elem'* \xe2\x86\x92 **elem < 10**\n+ * *Custom Expression on 'elem'* \xe2\x86\x92 ``elem < 10``\n \n * *Operate on elements* \xe2\x86\x92 **All**\n \n-**Note:** *There are actually simpler ways to achieve our purpose, but here we are demonstrating the use of a custom expression.*\n+**Note:** *There are actually simpler ways to achieve our purpose, but here we are demonstrating\n+the use of a custom expression.*\n \n After executing, we would then be presented with a table like so:\n \n@@ -1443,18 +1457,20 @@\n * *Input Single or Multiple Tables* \xe2\x86\x92 **Single Table**\n * *Column names on first row?* \xe2\x86\x92 **Yes**\n * *Row names on first column?* \xe2\x86\x92 **Yes**\n- * *Type of table operation* \xe2\x86\x92 **Compute Expression a"..b'values greater than 5, and set all\n+other values to 1.\n \n We have the following table:\n \n@@ -1483,13 +1499,11 @@\n * *Input Single or Multiple Tables* \xe2\x86\x92 **Single Table**\n * *Column names on first row?* \xe2\x86\x92 **Yes**\n * *Row names on first column?* \xe2\x86\x92 **Yes**\n- * *Type of table operation* \xe2\x86\x92 **Manipulate selected table elements**\n+ * *Type of table operation* \xe2\x86\x92 **Manipulate selected table elements**\n \n * *Operation to perform* \xe2\x86\x92 **Custom**\n \n- * *Custom Expression* \xe2\x86\x92 ::\n-\n- (math.log(elem) / elem) if (elem > 5) else 1\n+ * *Custom Expression* \xe2\x86\x92 ``(math.log(elem) / elem) if (elem > 5) else 1``\n \n * *Operate on elements* \xe2\x86\x92 **All**\n \n@@ -1508,7 +1522,8 @@\n g4 81 10 10\n === === === ===\n \n-and we want to subtract from each column the mean of that column divided by the standard deviation of it to yield:\n+and we want to subtract from each column the mean of that column divided by the standard\n+ deviation of it to yield:\n \n \n === ========= ========= =========\n@@ -1528,10 +1543,7 @@\n * *Type of table operation* \xe2\x86\x92 **Perform a Full Table Operation**\n \n * *Operation* \xe2\x86\x92 **Custom**\n-\n- * *Custom Expression on \'table\' along axis (0 or 1)* \xe2\x86\x92 ::\n-\n- table - table.mean(0)/table.std(0)\n+ * *Custom Expression on \'table\' along axis (0 or 1)* \xe2\x86\x92 ``table - table.mean(0)/table.std(0)``\n \n \n Example 6: Perform operations on multiple tables\n@@ -1658,8 +1670,8 @@\n * *Type of table operation* \xe2\x86\x92 **Perform a Full Table Operation**\n \n * *Operation* \xe2\x86\x92 **Melt**\n- * *Variable IDs* \xe2\x86\x92 "A"\n- * *Unpivoted IDs* \xe2\x86\x92 "B,C"\n+ * *Variable IDs* \xe2\x86\x92 ``A``\n+ * *Unpivoted IDs* \xe2\x86\x92 ``B,C``\n \n This converts the "B" and "C" columns into variables.\n \n@@ -1697,11 +1709,12 @@\n * *Type of table operation* \xe2\x86\x92 **Perform a Full Table Operation**\n \n * *Operation* \xe2\x86\x92 **Pivot**\n- * *Index* \xe2\x86\x92 "foo"\n- * *Column* \xe2\x86\x92 "bar"\n- * *Values* \xe2\x86\x92 "baz"\n+ * *Index* \xe2\x86\x92 ``foo``\n+ * *Column* \xe2\x86\x92 ``bar``\n+ * *Values* \xe2\x86\x92 ``baz``\n \n-This splits the matrix using "foo" and "bar" using only the values from "baz". Header values may contain extra information.\n+This splits the matrix using "foo" and "bar" using only the values from "baz". Header values\n+ may contain extra information.\n \n \n Example 9: Replacing text in specific rows or columns\n@@ -1739,23 +1752,21 @@\n \n * *Operation to perform* \xe2\x86\x92 **Replace values**\n \n- * *Replacement value* \xe2\x86\x92 ::\n-\n- chr{elem:.0f}\n+ * *Replacement value* \xe2\x86\x92 ``chr{elem:.0f}``\n \n- Here, the placeholder ``{elem}`` lets us refer to each element\'s\n- current value, while the ``:.0f`` part is a format specifier that makes\n- sure numbers are printed without decimals (for a complete description of\n- the available syntax see the\n+ Here, the placeholder ``{elem}`` lets us refer to each element\'s current value,\n+ while the ``:.0f`` part is a format specifier that makes sure numbers are printed\n+ without decimals (for a complete description of the available syntax see the\n `Python Format Specification Mini-Language <https://docs.python.org/3/library/string.html#formatspec>`_).\n \n * *Operate on elements* \xe2\x86\x92 **Specific Rows and/or Columns**\n- * *List of columns to select* \xe2\x86\x92 "2"\n- * *List of rows to select* \xe2\x86\x92 "2,4"\n- * *Inclusive Selection* \xe2\x86\x92 "No"\n+ * *List of columns to select* \xe2\x86\x92 ``2``\n+ * *List of rows to select* \xe2\x86\x92 ``2,4``\n+ * *Inclusive Selection* \xe2\x86\x92 ``No``\n \n \n-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:\n+If we wanted to instead add "chr" to the ALL elements in column 2 and rows 2 and 4, we\n+ would repeat the steps above but set the *Inclusive Selection* to "Yes", to give:\n \n === ===== ===== =====\n . c1 c2 c3\n@@ -1766,8 +1777,6 @@\n g4 chr81 chr6 chr3\n === ===== ===== =====\n \n-\n-\n ]]></help>\n <citations></citations>\n </tool>\n' |