Mercurial > repos > iuc > table_compute
diff table_compute.xml @ 0:1b0f96ed73f2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 1ee75135483d5db22c540bc043746cd986f85762"
| author | iuc |
|---|---|
| date | Sat, 17 Aug 2019 16:25:37 -0400 |
| parents | |
| children | dddadbbac949 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/table_compute.xml Sat Aug 17 16:25:37 2019 -0400 @@ -0,0 +1,1441 @@ +<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="@COPEN@"><![CDATA[<code>]]></token> + <token name="@CCLOSE@"><![CDATA[</code>]]></token> + <import>allowed_functions.xml</import> + <!-- text field validators --> + <macro name="validator_text" > + <validator type="regex" message="No special characters allowed">^(?:\w+)?$</validator> + <sanitizer sanitize="false" /> + </macro> + <macro name="validator_text_required" > + <validator type="regex" message="No special characters allowed">^(?:\w+)?$</validator> + <validator type="empty_field" /> + </macro> + <macro name="validator_index_identifiers" > + <validator type="regex" message="Specify a comma-separated list of index names without special characters">^(?:\w+(?:, *\w+)*)?$</validator> + <sanitizer sanitize="false" /> + </macro> + <macro name="validator_index_ranges"> + <validator type="regex" message="Specify a comma-separated list index numbers or ranges">^(?:\d+(?::\d)*(?:, *\d+(?::\d)*)*)?$</validator> + <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 '_ !-+=/*%.<>()'">^[\w !\-+=/*%,.<>()]+$</validator> + <sanitizer sanitize="false" /> + </macro> + <!-- macro for main input tests --> + <macro name="test_inputs_single" > + <conditional name="singtabop" > + <param name="use_type" value="single" /> + <param name="input" value="small.tsv" /> + <conditional name="user" > + <yield /> + </conditional> + </conditional> + </macro> + <!-- macro for umi to transcript tests --> + <macro name="umi2trans" > + <yield /> + <conditional name="user" > + <param name="mode" value="element" /> + <param name="element_op" value="gt" /> + <param name="element_value" value="0" /> + <conditional name="element" > + <param name="mode" value="custom" /> + <param name="custom_expr" value="-math.log(1 - elem/4096) * 4096 if elem != 4096 else elem - 0.5" /> + </conditional> + </conditional> + </macro> + <!-- macro for file inputs --> + <macro name="file_opts"> + <param name="input" type="data" format="tsv,tabular" label="Table" /> + <param name="col_row_names" type="select" display="checkboxes" multiple="true" optional="true" + label="This input data has"> + <option value="has_col_names" selected="true">Column names on the first row</option> + <option value="has_row_names" selected="true">Row names on the first column"</option> + </param> + </macro> + <!-- element value macro --> + <macro name="elem_val_macro" > + <param name="element_value" type="text" optional="true" label="Filter value" help="This value is converted to numeric if possible, otherwise it is treated as a string" /> + </macro> + </macros> + <requirements> + <requirement type="package" version="0.25">pandas</requirement> + <requirement type="package" version="1.17">numpy</requirement> + </requirements> + + <version_command><![CDATA[ + touch '$__tool_directory__/scripts/userconfig.py' && python '$__tool_directory__/scripts/table_compute.py' --version + ]]></version_command> + + <command detect_errors="exit_code"><![CDATA[ + ## Can only import generated userconfig.py if calling + ## script is in the same directory. Soft-linking does + ## not satisfy importing, so we copy everything. + cp '$userconf' ./userconfig.py && + cp '$__tool_directory__/scripts/safety.py' ./safety.py && + cp '$__tool_directory__/scripts/table_compute.py' ./table_compute.py && + python ./table_compute.py + ]]></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": $precision, + #if 'ignore_nas' in str($out_opts): + "narm": True, + #else: + "narm": False, + #end if + #if 'output_headers_row' in str($out_opts): + "out_headers_row": True, + #else: + "out_headers_row": False, + #end if + #if 'output_headers_col' in str($out_opts): + "out_headers_col": True, + #else: + "out_headers_col": False, + #end if + "user_mode": '$singtabop.use_type', + "outtable": '$table' +} + +#if str($singtabop.use_type) == "single": +Data = { + "tables": [ + { + "reader_file": '$singtabop.input', + #if 'has_col_names' in str($singtabop.col_row_names): + "reader_header": 0, + #else: + "reader_header": None, + #end if + #if 'has_row_names' in str($singtabop.col_row_names): + "reader_row_col": 0, + #else: + "reader_row_col": False, + #end if + } + ], + "params": { + "user_mode_single": '$singtabop.user.mode.value', + #if $singtabop.user.mode.value == 'precision': + ## Literally do nothing, the user just sets the precision slider + ## at the top default level + } + #elif $singtabop.user.mode.value == 'select': + "select_cols_unique": #echo 'select_cols_keepdupe' in str($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)), + #else + "select_cols_wanted": None, + #end if + #if $singtabop.user.select_rows_wanted: + "select_rows_wanted": $rangemake(str($singtabop.user.select_rows_wanted)), + #else + "select_rows_wanted": None, + #end if + } + #elif $singtabop.user.mode.value == 'filtersumval': + "filtersumval_mode": '$singtabop.user.filtersumval_mode.use.value', + "filtersumval_axis": $singtabop.user.axis.value, + #if $singtabop.user.filtersumval_mode.use.value == 'operation': + "filtersumval_compare": '$singtabop.user.filtersumval_mode.compare_op.value', + "filtersumval_op": '$singtabop.user.filtersumval_mode.operation.value', + "filtersumval_against": $singtabop.user.filtersumval_mode.against, + "filtersumval_minmatch": None, + #elif $singtabop.user.filtersumval_mode.use.value == 'element': + "filtersumval_compare": None, + "filtersumval_op": '$singtabop.user.filtersumval_mode.operation.value', + ## against could be string or float, so we parse this in the code + "filtersumval_against": '$singtabop.user.filtersumval_mode.against', + "filtersumval_minmatch": $singtabop.user.filtersumval_mode.minmatch, + #end if + } + #elif $singtabop.user.mode.value == 'matrixapply': + "matrixapply_dimension": $singtabop.user.dimension.value, + #if str($singtabop.user.matrixapply_func.vector_op) == 'custom': + #set $custom_func = str($singtabop.user.matrixapply_func.custom_func).strip() + "matrixapply_custom": True, + "matrixapply_custom_func": '$custom_func', + "matrixapply_op": None, + #else + "matrixapply_custom": False, + "matrixapply_custom_func": None, + "matrixapply_op": '$singtabop.user.matrixapply_func.vector_op', + #end if + } + #elif $singtabop.user.mode.value == 'element': + #if str($singtabop.user.elem_val.element_op) != "None": + "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": + "element_replace": '$singtabop.user.element.replace_value.value', + #elif str($singtabop.user.element.mode) == "modify": + "element_modify_op": '$singtabop.user.element.modify_op.value', + #elif str($singtabop.user.element.mode) == "scale": + "element_scale_op": '$singtabop.user.element.scale_op.value', + "element_scale_value": $singtabop.user.element.scale_value, + #elif str($singtabop.user.element.mode) == "custom": + #set $custom_func = str($singtabop.user.element.custom_expr).strip() + "element_customop": '$custom_func', + #end if + } + #elif $singtabop.user.mode.value == 'fulltable': + "mode": '$singtabop.user.general.use', + #if str($singtabop.user.general.use) == 'melt': + #if str($singtabop.user.general.id_vars).strip(): + #set $melt_ids = [i.strip() for i in str($singtabop.user.general.id_vars).split(',')] + #else + #set $melt_ids = 'None' + #end if + #if str($singtabop.user.general.value_vars).strip(): + #set $melt_values = [i.strip() for i in str($singtabop.user.general.value_vars).split(',')] + #else + #set $melt_values = 'None' + #end if + "MELT": { + "melt_ids": $melt_ids, + "melt_values": $melt_values, + }, + #elif str($singtabop.user.general.use) == 'pivot': + #set $pivot_index = str($singtabop.user.general.index).strip() + #if $pivot_index: + #set $pivot_index = "'" + $pivot_index + "'" + #else: + #set $pivot_index = 'None' + #end if + #set $pivot_column = "'" + str($singtabop.user.general.column).strip() + "'" + #if str($singtabop.user.general.values).strip(): + #set $pivot_values = [i.strip() for i in str($singtabop.user.general.values).split(',')] + #else + #set $pivot_values = 'None' + #end if + "PIVOT": { + "pivot_index": $pivot_index, + "pivot_column": $pivot_column, + "pivot_values": $pivot_values, + }, + #elif str($singtabop.user.general.use) == 'custom': + #set $custom_func = str($singtabop.user.general.fulltable_custom_expr.value).strip() + "fulltable_customop": '$custom_func', + + #end if + }, + #end if +} + +#elif str($singtabop.use_type) == "multiple": +#set $custom_func = str($singtabop.fulltable_custom_expr).strip() +Data = { + "tables": [ + #for $i, $s in enumerate($singtabop.tables) + { + "file": '${s.input}', + #if 'has_col_names' in str($s.col_row_names): + "header": 0, + #else: + "header": None, + #end if + #if 'has_row_names' in str($s.col_row_names): + "row_names": 0, + #else: + "row_names": False, + #end if + }, + #end for + ], + 'params': { + "fulltable_customop" : '$custom_func', + } +} +#end if + +]]> + </configfile> + </configfiles> + <inputs> + <conditional name="singtabop" > + <param name="use_type" type="select" label="Input Single or Multiple Tables" help="Operations on single tables are better tailored towards more general use-cases. For multiple tables usage, all tables should ideally be of the same dimensions for simple operations, although complex operations are also supported for unequally sized tables (see Help section)." > + <option value="single">Single Table</option> + <option value="multiple">Multiple Tables</option> + </param> + <when value="single"> + <expand macro="file_opts" /> + <conditional name="user" > + <param name="mode" type="select" label="Type of table operation" > + <option value="precision">No operation (just reformat on output)</option> + <option value="select">Drop, keep or duplicate rows and columns</option> + <option value="filtersumval">Filter rows or columns by their properties</option> + <option value="matrixapply">Compute expression across rows or columns</option> + <option value="element">Manipulate selected table elements</option> + <option value="fulltable">Perform a full table operation</option> + </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> + <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> + </param> + </when> + <when value="filtersumval" > + <param name="axis" type="select" display="radio" + label="Filter" > + <option value="1">Rows</option> + <option value="0">Columns</option> + </param> + <conditional name="filtersumval_mode" > + <param name="use" type="select" label="Filter criterion" help="See Example #2 for an example of using this mode." > + <option value="operation" >Result of function applied to columns/rows</option> + <option value="element" >Number of column/row elements passing filter</option> + </param> + <when value="operation"> + <param name="operation" type="select" label="Keep column/row if its observed" > + <expand macro="select_vectorops" /> + </param> + <param name="compare_op" type="select" label="is" > + <expand macro="select_twovaluebooleanops" /> + </param> + <param name="against" type="float" label="this value" value="0" /> + </when> + <when value="element"> + <param name="minmatch" type="integer" min="1" value="0" label="Keep column/row if at least" /> + <param name="operation" type="select" label="of its element are" > + <expand macro="select_twovaluebooleanops" > + <option value="str_eq" >~ (Matching)</option> + <option value="str_ne" >!~ (not Matching)</option> + </expand> + </param> + <param name="against" type="text" label="this value"> + <expand macro="validator_functiondef" /> + </param> + </when> + </conditional> + </when> + <when value="matrixapply" > + <conditional name="matrixapply_func"> + <param name="vector_op" type="select" label="Calculate"> + <option value="custom">Custom Function</option> + <expand macro="select_vectorops" > + <option value="rank">Ranks</option> + <option value="cumsum" >Cumulative Sum</option> + <option value="cumprod" >Cumulative Product</option> + <option value="cummin" >Cumulative Minimum</option> + <option value="cummax" >Cumulative Maximum</option> + </expand> + </param> + <when value="custom"> + <param name="custom_func" type="text" + label="Custom function on 'vec'" + help="The parameter name is @COPEN@vec@CCLOSE@, referring to a vector of a specific row or column being operated on. Numpy and Pandas DataFrame operators are supported. e.g. @COPEN@np.sum(vec) + np.median(vec)@CCLOSE@, and @COPEN@vec.sum() + vec.median()@CCLOSE@ are equivalent operations." > + <expand macro="validator_functiondef" /> + </param> + </when> + <when value="min" /> + <when value="max" /> + <when value="sum" /> + <when value="count" /> + <when value="nunique" /> + <when value="mean" /> + <when value="median" /> + <when value="std" /> + <when value="sem" /> + <when value="var" /> + <when value="mad" /> + <when value="product" /> + <when value="rank" /> + <when value="cumsum" /> + <when value="cumprod" /> + <when value="cummin" /> + <when value="cummax" /> + </conditional> + <param name="dimension" type="select" label="For each"> + <option value="0">Column</option> + <option value="1">Row</option> + </param> + </when> + <when value="fulltable"> + <conditional name="general" > + <param name="use" type="select" label="Operation" help="See Examples 5, 7, and 8 for usage" > + <option value="melt" >Melt</option> + <option value="pivot" >Pivot</option> + <option value="custom" >Custom</option> + </param> + <when value="melt" > + <param name="id_vars" type="text" value="" label="Variable IDs" + help="Comma-delimited list of column names to use as identifiers" > + <expand macro="validator_index_identifiers" /> + </param> + <param name="value_vars" type="text" value="" label="Unpivoted IDs" + help="Comma-delimited list of column names to un-pivot. Leave blank to use all." > + <expand macro="validator_index_identifiers" /> + </param> + </when> + <when value="pivot" > + <param name="index" type="text" value="" + label="Index" + help="Name of the column to use as new index" > + <expand macro="validator_text" /> + </param> + <param name="column" type="text" value="" + label="Column" + help="Name of the column to use to generate the columns of the new table from" > + <expand macro="validator_text_required" /> + </param> + <param name="values" type="text" value="" + label="Values" + help="Names of the columns to use for populating the cells of the new table. Leave blank to use all." > + <expand macro="validator_index_identifiers" /> + </param> + </when> + <when value="custom" > + <param name="fulltable_custom_expr" type="text" + label="Custom expression on 'table', along 'axis' (0 or 1)" + help="The parameter name is @COPEN@table@CCLOSE@ and @COPEN@axis@CCLOSE@, referring to the table being acted on and the column (@COPEN@0@CCLOSE@) or row (@COPEN@1@CCLOSE@) to perform the operation on. Numpy, math, Pandas DataFrame operators, and inline @COPEN@if else@CCLOSE@ are supported (e.g. @COPEN@np.log(table) - table.mean(0) / table.std(1)@CCLOSE@). See Example #5 in the Help section. "> + <expand macro="validator_functiondef" /> + </param> + </when> + </conditional> + </when> + <when value="element"> + <conditional name="element" > + <param name="mode" type="select" + label="Operation to perform" > + <option value="replace">Replace values</option> + <option value="modify">Transform</option> + <option value="scale">Arithmetic operation</option> + <option value="custom">Custom</option> + </param> + <when value="replace" > + <param name="replace_value" type="text" label="Replacement value" help="This value is converted to numeric if possible, otherwise it is treated as a string" /> + </when> + <when value="modify" > + <param name="modify_op" type="select" label="Transformation function" help="Example: to transform values to their square root, select @COPEN@Square Root@CCLOSE@ here."> + <expand macro="select_onevalueoperator" /> + </param> + </when> + <when value="scale"> + <param name="scale_op" type="select" label="Operation" help="The selected operation will be applied to the table elements as the first operand. The value of the second operand can be provided in the next box. Example: to raise all values to the power of 5, select @COPEN@Power@CCLOSE@ here and type @COPEN@5@CCLOSE@ in the box below." > + <expand macro="select_twovaluenumericoperator" /> + </param> + <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."> + <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." > + <expand macro="select_twovaluebooleanops" > + <option value="None" selected="true">All</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" /> + </when> + </conditional> + </when> + </conditional> + </when> + <when value="multiple"> + <repeat name="tables" title="Tables" min="1" default="1"> + <expand macro="file_opts" /> + </repeat> + <param name="fulltable_custom_expr" type="text" + label="Custom expression on 'tableN'" + help="The parameter name is @COPEN@tableN@CCLOSE@, where @COPEN@N@CCLOSE@ refers to a specific table. e.g. @COPEN@table1 + table3 - table2@CCLOSE@, will add the first and third input tables and then subtract the second. Most operators and @COPEN@if@CCLOSE@ @COPEN@else@CCLOSE@ statements are supported. See Example #6 in the Help section for further examples."> + <expand macro="validator_functiondef" /> + </param> + </when> + </conditional> + <param name="out_opts" type="select" display="checkboxes" multiple="true" optional="true" + label="Output formatting options"> + <option value="ignore_nas" selected="true">Ignore NA values</option> + <option value="output_headers_col" selected="true">Output column headers</option> + <option value="output_headers_row" selected="true">Output row headers</option> + </param> + <param name="precision" type="integer" min="0" max="20" value="6" label="Output decimal precision" /> + </inputs> + <outputs> + <data name="table" format="tabular" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <!-- Test 1: Select --> + <expand macro="test_inputs_single" > + <param name="mode" value="select" /> + <param name="select_cols_wanted" value="2:4,2,2" /> + <param name="select_rows_wanted" value="2:5,3,3" /> + <param name="select_keepdupe" value="select_cols_keepdupe" /> + </expand> + <param name="precision" value="2" /> + <output name="table" value="small.select.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 2: Select, cols only --> + <expand macro="test_inputs_single" > + <param name="mode" value="select" /> + <param name="select_cols_wanted" value="2:4,2,2" /> + <param name="select_keepdupe" value="select_cols_keepdupe,select_rows_keepdupe" /> + </expand> + <param name="precision" value="2" /> + <output name="table" value="small.select.colsonly.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 3: Select, rows only --> + <expand macro="test_inputs_single" > + <param name="mode" value="select" /> + <param name="select_rows_wanted" value="2:5,3,3" /> + <param name="select_keepdupe" value="select_cols_keepdupe" /> + </expand> + <param name="precision" value="2" /> + <output name="table" value="small.select.rowsonly.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 4: Filtersumval, row --> + <expand macro="test_inputs_single" > + <param name="mode" value="filtersumval" /> + <param name="axis" value="1" /> + <conditional name="filtersumval_mode" > + <param name="use" value="operation" /> + <param name="operation" value="sum" /> + <param name="compare_op" value="gt" /> + <param name="against" value="50" /> + </conditional> + </expand> + <param name="precision" value="2" /> + <output name="table" value="small.fs.rowsum.gt.50.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 5: Filtersumval, col neq 0 --> + <expand macro="test_inputs_single" > + <param name="mode" value="filtersumval" /> + <param name="axis" value="0" /> + <conditional name="filtersumval_mode" > + <param name="use" value="operation" /> + <param name="operation" value="sum" /> + <param name="compare_op" value="ne" /> + <param name="against" value="0" /> + </conditional> + </expand> + <param name="precision" value="2" /> + <output name="table" value="small.fs.colsum.neq0.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 6: Filtersumval, col val gt 10 --> + <expand macro="test_inputs_single" > + <param name="mode" value="filtersumval" /> + <param name="axis" value="0" /> + <conditional name="filtersumval_mode" > + <param name="use" value="operation" /> + <param name="operation" value="sum" /> + <param name="compare_op" value="gt" /> + <param name="against" value="10" /> + </conditional> + </expand> + <param name="precision" value="2" /> + <output name="table" value="small.fs.colsum.gt10.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 7: Filtersumval, median val col >= 2 --> + <expand macro="test_inputs_single" > + <param name="mode" value="filtersumval" /> + <param name="axis" value="0" /> + <conditional name="filtersumval_mode" > + <param name="use" value="operation" /> + <param name="operation" value="median" /> + <param name="compare_op" value="ge" /> + <param name="against" value="2" /> + </conditional> + </expand> + <param name="precision" value="5" /> + <output name="table" value="small.fs.medvalcol.ge2.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 8: Filtersumval, keep rows with at least + two values > 2 --> + <expand macro="test_inputs_single" > + <param name="mode" value="filtersumval" /> + <param name="axis" value="1" /> + <conditional name="filtersumval_mode" > + <param name="use" value="element" /> + <param name="operation" value="gt" /> + <param name="against" value="2" /> + <param name="minmatch" value="2" /> + </conditional> + </expand> + <param name="precision" value="5" /> + <output name="table" value="small.fs.elemgt2.mm2.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 9: Filtersumval, keep cols with at least + 4 string values matching "0" --> + <expand macro="test_inputs_single" > + <param name="mode" value="filtersumval" /> + <param name="axis" value="0" /> + <conditional name="filtersumval_mode" > + <param name="use" value="element" /> + <param name="operation" value="str_ne" /> + <param name="against" value="0" /> + <param name="minmatch" value="4" /> + </conditional> + </expand> + <param name="precision" value="3" /> + <output name="table" value="small.fs.elemnmatch0.mm4.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 10: Matrix Apply, row max --> + <expand macro="test_inputs_single" > + <param name="mode" value="matrixapply" /> + <param name="dimension" value="1" /> + <conditional name="matrixapply_func" > + <param name="vector_op" value="max" /> + </conditional> + </expand> + <param name="precision" value="0" /> + <param name="out_opts" value="ignore_nas,output_headers_row" /> + <output name="table" value="small.matapp.rowmax.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 11: Element, all, scale, remainder 5 --> + <expand macro="test_inputs_single" > + <param name="mode" value="element" /> + <conditional name="elem_val"> + <param name="element_op" value="None" /> + </conditional> + <conditional name="element" > + <param name="mode" value="scale" /> + <param name="scale_op" value="mod" /> + <param name="scale_value" value="5" /> + </conditional> + </expand> + <param name="precision" value="2" /> + <output name="table" value="small.element.scalerem5.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 12: Matrix Apply, column custom --> + <expand macro="test_inputs_single" > + <param name="mode" value="matrixapply" /> + <param name="dimension" value="0" /> + <conditional name="matrixapply_func" > + <param name="vector_op" value="custom" /> + <param name="custom_func" value="vec.sum()+vec.median()" /> + </conditional> + </expand> + <param name="precision" value="2" /> + <param name="out_opts" value="ignore_nas,output_headers_row" /> + <output name="table" value="small.matapp.colcust.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 13: Element, non-zero, custom --> + <expand macro="test_inputs_single" > + <param name="mode" value="element" /> + <conditional name="elem_val"> + <param name="element_op" value="gt" /> + <param name="element_value" value="0" /> + </conditional> + <conditional name="element" > + <param name="mode" value="custom" /> + <!-- valid complex expression for non-zero vals --> + <param name="custom_expr" value="(math.log10(elem)+elem)/elem if (elem < math.inf) else 1.0" /> + </conditional> + </expand> + <output name="table" value="small.element.custom.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 14: umi2transcript test1 --> + <expand macro="umi2trans" > + <param name="input" value="mat1.umi.tsv" /> + <output name="table" value="mat1.trans.tsv" /> + </expand> + </test> + <test expect_num_outputs="1"> + <!-- Test 15: umi2transcript test2 --> + <expand macro="umi2trans" > + <param name="input" value="mat2.umi.tsv" /> + <output name="table" value="mat2.trans.tsv" /> + </expand> + </test> + <test expect_num_outputs="1"> + <!-- Test 16: B-test - mean and sd in custom func --> + <expand macro="test_inputs_single" > + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="custom" /> + <param name="fulltable_custom_expr" + value="table - table.mean(0) / table.std(0)" /> + </conditional> + </expand> + <output name="table" value="small.fulltable.tsv" /> + </test> + <test expect_num_outputs="1"> + <!-- Test 17: Multiple table test --> + <conditional name="singtabop" > + <param name="use_type" value="multiple" /> + <repeat name="tables"> + <param name="input" value="small.tsv" /> + </repeat> + <repeat name="tables"> + <param name="input" value="small.tsv" /> + </repeat> + <repeat name="tables"> + <param name="input" value="small.tsv" /> + </repeat> + <param name="fulltable_custom_expr" value="(3 * table1) + np.log(table3 + 20) - table2" /> </conditional> + <output name="table" value="small.multiple.tsv" /> + </test> + <!-- User tests that failed previously --> + <test expect_num_outputs="1"> + <!-- Test 18 --> + <expand macro="test_inputs_single" > + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="custom" /> + <param name="fulltable_custom_expr" value="table * 2" /> + </conditional> + </expand> + <output name="table" > + <assert_contents> + <has_n_columns n="10" /> + <has_line_matching expression="^gene1\s20\.000000\s0\s12\s-20\.200000\s20\s2\.200000\s0\.000000\s0\s0\.000000$" /> + <has_line_matching expression="gene5\s2\.000000\s0\s0\s-20\.000000\s880\s12\.000000\s0\.000000\s0\s3\.800000" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <!-- Test 19 --> + <expand macro="test_inputs_single" > + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="custom" /> + <param name="fulltable_custom_expr" value="table == 5" /> + </conditional> + </expand> + <output name="table" > + <assert_contents> + <has_n_columns n="10" /> + <has_line_matching expression="^gene1(\sFalse)+$" /> + <has_line_matching expression="gene5(\sFalse)+$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" expect_failure="true"> + <!-- Test 20 --> + <expand macro="test_inputs_single" > + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="custom" /> + <param name="fulltable_custom_expr" value="for n in table: n = n + 1" /> + </conditional> + </expand> + </test> + <test expect_num_outputs="1" expect_failure="true"> + <!-- Test 21 --> + <expand macro="test_inputs_single" > + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="custom" /> + <param name="fulltable_custom_expr" value="table + table[0,0]" /> + </conditional> + </expand> + </test> + <test expect_num_outputs="1"> + <!-- Test 22: Melt --> + <expand macro="test_inputs_single" > + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="melt" /> + <param name="id_vars" value="cell1,cell3" /> + <param name="value_vars" value="cell5,cell6" /> + </conditional> + </expand> + <param name="out_opts" value="ignore_nas,output_headers_col" /> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^cell1\scell3\svariable\svalue$" /> + <has_line_matching expression="^1\.0+\s0+\scell6\s6\.0+$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <!-- Test 23: Pivot --> + <expand macro="test_inputs_single" > + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="pivot" /> + <param name="index" value="cell1" /> + <param name="column" value="cell2" /> + <param name="values" value="cell3,cell7,cell9" /> + </conditional> + </expand> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^\scell3\scell7\scell9$" /> + <has_line_matching expression="^1\.0+\s0\.0+\s0\.0+\s1\.90+$" /> + <has_line_matching expression="^10\.0+\s6\.0+\s0\.0+\s0\.0+$" /> + </assert_contents> + </output> + </test> + <!-- Add Example Text Tests --> + <test expect_num_outputs="1" > + <!-- Test 24: Ex 1 --> + <conditional name="singtabop" > + <param name="use_type" value="single" /> + <param name="input" value="examples.1.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + <conditional name="user" > + <param name="mode" value="select" /> + <param name="select_cols_wanted" value="1,1,3" /> + <param name="select_rows_wanted" value="1:3,2" /> + <param name="select_keepdupe" value="select_cols_keepdupe,select_rows_keepdupe" /> + </conditional> + </conditional> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^\s+c1\s+c1\s+c3$" /> + <has_line_matching expression="^g2\s+3\s+3\s+9$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Test 25: Ex 2 --> + <conditional name="singtabop" > + <param name="use_type" value="single" /> + <param name="input" value="examples.2.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + <conditional name="user" > + <param name="mode" value="filtersumval" /> + <param name="axis" value="1" /> + <conditional name="filtersumval_mode" > + <param name="use" value="operation" /> + <param name="operation" value="sum" /> + <param name="compare_op" value="lt" /> + <param name="against" value="50" /> + </conditional> + </conditional> + </conditional> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^\s+c1\s+c2\s+c3$" /> + <has_line_matching expression="^g3\s+4\s+8\s+12$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Test 26: Ex 3_P1 --> + <conditional name="singtabop" > + <param name="use_type" value="single" /> + <param name="input" value="examples.3p1.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + <conditional name="user" > + <param name="mode" value="element" /> + <conditional name="element" > + <param name="mode" value="custom" /> + <param name="custom_expr" value="elem < 10" /> + </conditional> + <conditional name="elem_val" > + <param name="element_op" value="None" /> + </conditional> + </conditional> + </conditional> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^g1\s+False\s+False\s+False$" /> + <has_line_matching expression="^g4\s+False\s+True\s+True$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Test 27: Ex 3_P2 --> + <conditional name="singtabop" > + <param name="use_type" value="single" /> + <param name="input" value="examples.3p2.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + <conditional name="user" > + <param name="mode" value="matrixapply" /> + <param name="dimension" value="1" /> + <conditional name="matrixapply_func" > + <param name="vector_op" value="sum" /> + </conditional> + </conditional> + </conditional> + <output name="table" > + <assert_contents> + <has_n_columns n="2" /> + <has_line_matching expression="^g1\s+0$" /> + <has_line_matching expression="^g4\s+2$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Test 28: Ex 4 --> + <conditional name="singtabop" > + <param name="use_type" value="single" /> + <param name="input" value="examples.4.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + <conditional name="user" > + <param name="mode" value="element" /> + <conditional name="element" > + <param name="mode" value="custom" /> + <param name="custom_expr" value="(math.log(elem) / elem) if (elem > 5) else 1" /> + </conditional> + <conditional name="elem_val" > + <param name="element_op" value="All" /> + </conditional> + </conditional> + </conditional> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^g1\s+1\.00\d+\s+0\.149\d+\s+0\.113\d+$" /> + <has_line_matching expression="^g4\s+0\.05\d+\s+1\.000\d+\s+1\.000\d+$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Test 29: Ex 5 --> + <conditional name="singtabop" > + <param name="use_type" value="single" /> + <param name="input" value="examples.5.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + <conditional name="user" > + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="custom" /> + <param name="fulltable_custom_expr" value="table - table.mean(0)/table.std(0)" /> + </conditional> + </conditional> + </conditional> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^g1\s+9\.\d+\s+17\.\d+\s+28\.\d+$" /> + <has_line_matching expression="^g4\s+80\.\d+\s+7\.\d+\s+8\.\d+$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Test 30: Ex 6 --> + <conditional name="singtabop" > + <param name="use_type" value="multiple" /> + <repeat name="tables" > + <param name="input" value="examples.6p1.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + </repeat> + <repeat name="tables" > + <param name="input" value="examples.6p2.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + </repeat> + <repeat name="tables" > + <param name="input" value="examples.6p3.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + </repeat> + <param name="fulltable_custom_expr" value="table1 / min(np.max(np.max(table2)), np.max(np.max(table3)))" /> + </conditional> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^g1\s+3\.3\d+\s+6\.6\d+\s+10\.0\d+$" /> + <has_line_matching expression="^g3\s+1\.3\d+\s+2\.6\d+\s+3\.3\d+$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Test 31: Ex 7 --> + <conditional name="singtabop" > + <param name="use_type" value="single" /> + <param name="input" value="examples.7.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + <conditional name="user"> + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="melt" /> + <param name="id_vars" value="A" /> + <param name="value_vars" value="B,C" /> + </conditional> + </conditional> + </conditional> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^0\s+a\s+B\s+B\s*$" /> + <has_line_matching expression="^5\s+c\s+C\s+5\s*$" /> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1" > + <!-- Test 32: Ex 8 --> + <conditional name="singtabop" > + <param name="use_type" value="single" /> + <param name="input" value="examples.8.tsv" /> + <param name="col_row_names" value="has_col_names,has_row_names" /> + <conditional name="user" > + <param name="mode" value="fulltable" /> + <conditional name="general" > + <param name="use" value="pivot" /> + <param name="index" value="foo" /> + <param name="column" value="bar" /> + <param name="values" value="baz" /> + </conditional> + </conditional> + </conditional> + <output name="table" > + <assert_contents> + <has_n_columns n="4" /> + <has_line_matching expression="^one\s+1\s+2\s+3$" /> + <has_line_matching expression="^two\s+4\s+5\s+6$" /> + </assert_contents> + </output> + </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. + +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. + + + +Examples +======== + +Example 1: Sub-selecting from a table +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +We have the following table: + + === === === === + . c1 c2 c3 + === === === === + g1 10 20 30 + 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: + + === === === === + . c1 c1 c3 + === === === === + g1 10 10 30 + g2 3 3 9 + g3 4 4 12 + g2 3 3 9 + === === === === + +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** + + * *List of columns to select* → **1,1,3** + * *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 +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +We have the following table: + + === === === === + . c1 c2 c3 + === === === === + g1 10 20 30 + g2 3 6 9 + g3 4 8 12 + g4 81 6 3 + === === === === + +and we want: + + === === === === + . c1 c2 c3 + === === === === + g2 3 6 9 + g3 4 8 12 + === === === === + +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** + + * *Filter* → **Rows** + * *Filter Criterion* → **Result of function applied to columns/rows** + + * *Keep column/row if its observed* → **Sum** + * *is* → **< (Less Than)** + * *this value* → **50** + + +Example 3: Count the number of values per row smaller than a specified value +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +We have the following table: + + === === === === + . c1 c2 c3 + === === === === + g1 10 20 30 + g2 3 6 9 + g3 4 8 12 + g4 81 6 3 + === === === === + +and we want to count how many elements in each row are smaller than 10, i.e., +we want to obtain the following results table: + + === === + . vec + === === + g1 0 + g2 3 + g3 2 + g4 2 + === === + +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 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.* + +After executing, we would then be presented with a table like so: + + === ===== ===== ===== + . c1 c2 c3 + === ===== ===== ===== + g1 False False False + g2 True True True + g3 True True False + g4 False True True + === ===== ===== ===== + +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** + + * *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). + + +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 have the following table: + + === === === === + . c1 c2 c3 + === === === === + g1 0 20 30 + g2 3 0 9 + g3 4 8 0 + g4 81 0 0 + === === === === + +and we want: + + === ========== ========= ========= + . c1 c2 c3 + === ========== ========= ========= + g1 1.00000000 0.1497866 0.1133732 + g2 1.00000000 1.0000000 0.2441361 + g3 1.00000000 0.2599302 1.0000000 + g4 0.05425246 1.0000000 1.0000000 + === ========== ========= ========= + +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* → :: + + (math.log(elem) / elem) if (elem > 5) else 1 + + * *Operate on elements* → **All** + + +Example 5: Perform a Full table operation +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +We have the following table: + + === === === === + . c1 c2 c3 + === === === === + g1 10 20 30 + 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: + + + === ========= ========= ========= + . c1 c2 c3 + === ========= ========= ========= + g1 9.351737 17.784353 28.550737 + g2 2.351737 7.784353 7.550737 + g3 3.351737 5.784353 8.550737 + g4 80.351737 7.784353 8.550737 + === ========= ========= ========= + +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* → **Perform a Full Table Operation** + + * *Operation* → **Custom** + + * *Custom Expression on 'table' along axis (0 or 1)* → :: + + table - table.mean(0)/table.std(0) + + +Example 6: Perform operations on multiple tables +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +We have the following three input tables: + +Table 1 + + === === === === + . c1 c2 c3 + === === === === + g1 10 20 30 + g2 3 10 9 + g3 4 8 10 + === === === === + +Table 2 + + === === === + . c1 c2 + === === === + g1 1 2 + g2 3 4 + g3 6 5 + === === === + +Table 3 + + === === === === + . c1 c2 c3 + === === === === + g1 1 2 3 + g2 1 2 3 + === === === === + + +*Note that the dimensions of these tables do not match.* + +Dimensions: + * Table1 [3,3] + * Table2 [3,2] + * Table3 [2,3] + +In order to perform simple operations between Tables, they must be of the same dimensions. + +To add Table2 to Table3 we would have to transpose one of the tables using the in-built `T` method:: + + table2 + table3.T + +or:: + + table2.T + table3 + +We can also perform more general operations using all 3 tables, such as taking the minimum value of +the maximum values of Table2 and Table3, and dividing the Table1 values by it:: + + table1 / min(table2.values.max(), table3.values.max()) + + +To perform these types of operations in Galaxy we would select the following: + + * *Input Single or Multiple Tables* → **Multiple Tables** + * *(For each inserted table)* + * *Column names on first row?* → **Yes** + * *Row names on first column?* → **Yes** + * *Custom Expression* → :: + + <insert your desired function> + +Please note that the last example shown above was chosen to illustrate the +limitations of the tool. Nested attributes like `table2.values.max` are +disallowed in expressions in the tool so the above would have to be replaced +with the harder to read workaround:: + + table1 / min(np.max(np.max(table2)), np.max(np.max(table3))) + +Also note that, currently `min()`, `max()` and `sum()` are the only built-in +Python functions that can be used inside expressions. If you want to use +additional functions, these have to be qualified functions from the `math`, +`np` or `pd` libraries. + + +Example 7: Melt +~~~~~~~~~~~~~~~ + +We have the following table + + === === === === + . A B C + === === === === + 0 a B 1 + 1 b B 3 + 2 c B 5 + === === === === + +and we want: + + === === ======== ===== + . A variable value + === === ======== ===== + 0 a B B + 1 b B B + 2 c B B + 3 a C 1 + 4 b C 3 + 5 c C 5 + === === ======== ===== + + +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* → **Perform a Full Table Operation** + + * *Operation* → **Melt** + * *Variable IDs* → "A" + * *Unpivoted IDs* → "B,C" + +This converts the "B" and "C" columns into variables. + + +Example 8: Pivot +~~~~~~~~~~~~~~~~ + +We have the following table + + === === === === === + . foo bar baz zoo + === === === === === + 0 one A 1 x + 1 one B 2 y + 2 one C 3 z + 3 two A 4 q + 4 two B 5 w + 5 two C 6 t + === === === === === + +and we want: + + === === === === + . A B C + === === === === + one 1 2 3 + two 4 5 6 + === === === === + +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* → **Perform a Full Table Operation** + + * *Operation* → **Pivot** + * *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. + +]]></help> + <citations></citations> +</tool>