table_compute: table_compute.xml comparison

comparison table_compute.xml @ 2:fd9f92324423 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit d00a518202228b990aeeea2ec3f842501fd2ec09"

author	iuc
date	Fri, 13 Sep 2019 14:54:16 -0400
parents	9190f11e46cd
children	133d6fd96765

comparison

equal deleted inserted replaced

-:9190f11e46cd
+:fd9f92324423
 <tool id="table_compute" name="Table Compute" version="@VERSION@">
 <description>computes operations on table data</description>
 <macros>
-<token name="@VERSION@">0.9.1</token>
+<token name="@VERSION@">0.9.2</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" >
 <macro name="validator_index_ranges">
 <validator type="regex" message="Specify a comma-separated list index numbers or ranges">^(?:-?\d+(?::-?\d+)*(?:, *-?\d+(?::-?\d+)*)*)?$</validator>
 <sanitizer sanitize="false" />
 </macro>
 <macro name="validator_functiondef">
-<validator type="regex" message="An expression is required and is allowed to contain only letters, numbers and the characters '_ !-+=/*%.&lt;&gt;()'">^['"\w !\-+=/*%,.&lt;&gt;()]+$</validator>
+<validator type="regex" message="An expression is required and is allowed to contain only letters, numbers and the characters _ !-+=/*%.&lt;&gt;()">^[\w !\-+=/*%,.&lt;&gt;()]+$</validator>
 <sanitizer sanitize="false" />
 </macro>
 <!-- macro for main input tests -->
 <macro name="test_inputs_single" >
 <conditional name="singtabop" >
 <!-- macro for umi to transcript tests -->
 <macro name="umi2trans" >
 <yield />
 <conditional name="user" >
 <param name="mode" value="element" />
-<param name="element_op" value="gt" />
+<conditional name="elem_val">
-<param name="element_value" value="0" />
+<param name="element_op" value="None" />
+</conditional>
 <conditional name="element" >
 <param name="mode" value="custom" />
 <param name="custom_expr" value="-math.log(1 - elem/4096) * 4096 if elem != 4096 else elem - 0.5" />
 </conditional>
 </conditional>
 "user_mode": '$singtabop.use_type',
 "outtable": '$table'
 }
 #if str($singtabop.use_type) == "single":
+#set $op_mode = str($singtabop.user.mode)
 Data = {
 "tables": [
 {
 "file": '$singtabop.input',
 #if $singtabop.adv.header:
 "nrows": None,
 #end if
 }
 ],
 "params": {
-"user_mode_single": '$singtabop.user.mode.value',
+"user_mode_single": '$op_mode',
-#if $singtabop.user.mode.value == 'precision':
+#if $op_mode == 'precision':
 ## Literally do nothing, the user just sets the precision slider
 ## at the top default level
 }
-#elif $singtabop.user.mode.value == 'select':
+#elif $op_mode == 'select':
 "select_cols_unique": #echo 'select_cols_keepdupe' in str($singtabop.user.select_keepdupe)#,
 "select_rows_unique": #echo 'select_rows_keepdupe' in str($singtabop.user.select_keepdupe)#,
 #if $singtabop.user.select_cols_wanted:
 "select_cols_wanted": '$singtabop.user.select_cols_wanted',
 #else
 "select_rows_wanted": '$singtabop.user.select_rows_wanted',
 #else
 "select_rows_wanted": None,
 #end if
 }
-#elif $singtabop.user.mode.value == 'filtersumval':
+#elif $op_mode == 'filtersumval':
-"filtersumval_mode": '$singtabop.user.filtersumval_mode.use.value',
+#set $filter_type = str($singtabop.user.filtersumval_mode.use)
-"filtersumval_axis": $singtabop.user.axis.value,
+"filtersumval_mode": '$filter_type',
-#if $singtabop.user.filtersumval_mode.use.value == 'operation':
+"filtersumval_axis": $singtabop.user.axis,
-"filtersumval_compare": '$singtabop.user.filtersumval_mode.compare_op.value',
+#if $filter_type == 'operation':
-"filtersumval_op": '$singtabop.user.filtersumval_mode.operation.value',
+"filtersumval_compare": '$singtabop.user.filtersumval_mode.compare_op',
+"filtersumval_op": '$singtabop.user.filtersumval_mode.operation',
 "filtersumval_against": $singtabop.user.filtersumval_mode.against,
 "filtersumval_minmatch": None,
-#elif $singtabop.user.filtersumval_mode.use.value == 'element':
+#elif $filter_type == 'element':
 "filtersumval_compare": None,
-"filtersumval_op": '$singtabop.user.filtersumval_mode.operation.value',
+"filtersumval_op": '$singtabop.user.filtersumval_mode.operation',
 ## against could be string or float, so we parse this in the code
 "filtersumval_against": '$singtabop.user.filtersumval_mode.against',
 "filtersumval_minmatch": $singtabop.user.filtersumval_mode.minmatch,
 #end if
 }
-#elif $singtabop.user.mode.value == 'matrixapply':
+#elif $op_mode == 'matrixapply':
-"matrixapply_dimension": $singtabop.user.dimension.value,
+"matrixapply_dimension": $singtabop.user.dimension,
 #if str($singtabop.user.matrixapply_func.vector_op) == 'custom':
 #set $custom_func = str($singtabop.user.matrixapply_func.custom_func).strip()
 "matrixapply_custom": True,
 "matrixapply_custom_func": '$custom_func',
 "matrixapply_op": None,
 "matrixapply_custom": False,
 "matrixapply_custom_func": None,
 "matrixapply_op": '$singtabop.user.matrixapply_func.vector_op',
 #end if
 }
-#elif $singtabop.user.mode.value == 'element':
+#elif $op_mode == 'element':
-#if str($singtabop.user.elem_val.element_op) == "None":
+#set $filter_type = str($singtabop.user.elem_val.element_op)
+#set $element_mode = str($singtabop.user.element.mode)
+#if $filter_type == "None":
 "element_op": None,
-#elif str($singtabop.user.elem_val.element_op) == "rowcol":
+#elif $filter_type == "rowcol":
 "element_op": "rowcol",
 #if $singtabop.user.elem_val.select_rows_wanted
 "element_rows": '$singtabop.user.elem_val.select_rows_wanted',
 #end if
 #if $singtabop.user.elem_val.select_cols_wanted
 "element_cols": '$singtabop.user.elem_val.select_cols_wanted',
 #end if
 "element_inclusive": $singtabop.user.elem_val.inclusive_selection,
 #else:
-"element_op": '$singtabop.user.elem_val.element_op.value',
+"element_op": '$filter_type',
 ## Value is string or float, parsed in code later
 "element_value" : '$singtabop.user.elem_val.element_value',
 #end if
-"element_mode": '$singtabop.user.element.mode.value',
+"element_mode": '$element_mode',
-#if str($singtabop.user.element.mode) == "replace":
+#if $element_mode == "replace":
-"element_replace": '$singtabop.user.element.replace_value.value',
+"element_replace": '$singtabop.user.element.replace_value',
-#elif str($singtabop.user.element.mode) == "modify":
+#elif $element_mode == "modify":
-"element_modify_op": '$singtabop.user.element.modify_op.value',
+"element_modify_op": '$singtabop.user.element.modify_op',
-#elif str($singtabop.user.element.mode) == "scale":
+#elif $element_mode == "scale":
-"element_scale_op": '$singtabop.user.element.scale_op.value',
+"element_scale_op": '$singtabop.user.element.scale_op',
 "element_scale_value": $singtabop.user.element.scale_value,
-#elif str($singtabop.user.element.mode) == "custom":
+#elif $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':
+#elif $op_mode == 'fulltable':
 "mode": '$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
 "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()
+#set $custom_func = str($singtabop.user.general.fulltable_custom_expr).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}',
 </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="transpose">Transpose</option>
-<option value="pivot" >Pivot</option>
+<option value="melt">Melt</option>
-<option value="custom" >Custom</option>
+<option value="pivot">Pivot</option>
+<option value="custom">Custom</option>
 </param>
+<when value="transpose" />
 <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>
 <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" />
+<param name="replace_value" type="text" label="Replacement value" help="If you want to reuse the current value of each element as part of the  replacement value, you can refer to it using the special @COPEN@{elem}@CCLOSE@ placeholder (see Example #9 in the Help section).">
+<sanitizer>
+<valid>
+<add value="{" />
+<add value="}" />
+</valid>
+</sanitizer>
+</param>
 </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>
 <param name="fulltable_custom_expr" value="table + table[0,0]" />
 </conditional>
 </expand>
 </test>
 <test expect_num_outputs="1">
-<!-- Test 22: Melt -->
+<!-- Test 22: Transpose -->
+<expand macro="test_inputs_single" >
+<param name="mode" value="fulltable" />
+<conditional name="general" >
+<param name="use" value="transpose" />
+</conditional>
+</expand>
+<param name="out_opts" value="ignore_nas,output_headers_col" />
+<output name="table" >
+<assert_contents>
+<has_n_columns n="5" />
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- Test 23: 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" />
 <has_line_matching expression="^1\.0+\s0+\scell6\s6\.0+$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1">
-<!-- Test 23: Pivot -->
+<!-- Test 24: Pivot -->
 <expand macro="test_inputs_single" >
 <param name="mode" value="fulltable" />
 <conditional name="general" >
 <param name="use" value="pivot" />
 <param name="index" value="cell1" />
 </assert_contents>
 </output>
 </test>
 <!-- Add Example Text Tests -->
 <test expect_num_outputs="1" >
-<!-- Test 24: Ex 1 -->
+<!-- Test 25: 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" >
 <has_line_matching expression="^g2\s+3\s+3\s+9$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 25: Ex 2 -->
+<!-- Test 26: Ex 2 -->
 <conditional name="singtabop" >
 <param name="use_type" value="single" />
 <param name="input" value="examples.2.tsv" />
 <param name="col_row_names" value="has_col_names,has_row_names" />
 <conditional name="user" >
 <has_line_matching expression="^g3\s+4\s+8\s+12$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 26: Ex 3_P1 -->
+<!-- Test 27: 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" >
 <has_line_matching expression="^g4\s+False\s+True\s+True$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 27: Ex 3_P2 -->
+<!-- Test 28: Ex 3_P2 -->
 <conditional name="singtabop" >
 <param name="use_type" value="single" />
 <param name="input" value="examples.3p2.tsv" />
 <param name="col_row_names" value="has_col_names,has_row_names" />
 <conditional name="user" >
 <has_line_matching expression="^g4\s+2$" />
 </assert_contents>
 </output>
 	        </test>
 <test expect_num_outputs="1" >
-<!-- Test 28: Ex 4 -->
+<!-- Test 29: 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" >
 <has_line_matching expression="^g4\s+0\.05\d+\s+1\.000\d+\s+1\.000\d+$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 29: Ex 5 -->
+<!-- Test 30: Ex 5 -->
 <conditional name="singtabop" >
 <param name="use_type" value="single" />
 <param name="input" value="examples.5.tsv" />
 <param name="col_row_names" value="has_col_names,has_row_names" />
 <conditional name="user" >
 <has_line_matching expression="^g4\s+80\.\d+\s+7\.\d+\s+8\.\d+$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 30: Ex 6 -->
+<!-- Test 31: 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" />
 <has_line_matching expression="^g3\s+1\.3\d+\s+2\.6\d+\s+3\.3\d+$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 31: Ex 7 -->
+<!-- Test 32: Ex 7 -->
 <conditional name="singtabop" >
 <param name="use_type" value="single" />
 <param name="input" value="examples.7.tsv" />
 <param name="col_row_names" value="has_col_names,has_row_names" />
 <conditional name="user">
 <has_line_matching expression="^5\s+c\s+C\s+5\s*$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 32: Ex 8 -->
+<!-- Test 33: 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" >
 <has_line_matching expression="^two\s+4\s+5\s+6$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 33: Subtracting table means #1 -->
+<!-- Test 34: Negative range test #1 -->
-<conditional name="singtabop" >
-<param name="use_type" value="single" />
-<param name="input" value="examples.5.tsv" />
-<param name="col_row_names" value="has_col_names,has_row_names" />
-<conditional name="user" >
-<param name="mode" value="fulltable" />
-<conditional name="general" >
-<param name="use" value="custom" />
-<param name="fulltable_custom_expr" value="table - table.mean(1)/table.std(1)" />
-</conditional>
-</conditional>
-</conditional>
-<output name="table" >
-<assert_contents>
-<has_n_columns n="8" />
-<!-- should give nonsense empty output -->
-<has_line_matching expression="^\sc1\sc2\sc3\sg1\sg2\sg3\sg4$" />
-<has_line_matching expression="^g4\s+$" />
-</assert_contents>
-</output>
-</test>
-<test expect_num_outputs="1" >
-<!-- Test 34: Subtracting table means #2 -->
-<conditional name="singtabop" >
-<param name="use_type" value="single" />
-<param name="input" value="examples.5.tsv" />
-<param name="col_row_names" value="has_col_names,has_row_names" />
-<conditional name="user" >
-<param name="mode" value="fulltable" />
-<conditional name="general" >
-<param name="use" value="custom" />
-<param name="fulltable_custom_expr" value="table.sub(table.mean(1), 0).div(table.std(1),0)" />
-</conditional>
-</conditional>
-</conditional>
-<output name="table" >
-<assert_contents>
-<has_n_columns n="4" />
-<has_line_matching expression="^g1\s+-1\.\d+\s+0\.\d+\s+1\.\d+\s*$" />
-<has_line_matching expression="^g4\s+1\.1\d+\s+-0\.5\d+\s+-0\.5\d+\s*$" />
-</assert_contents>
-</output>
-</test>
-<test expect_num_outputs="1" >
-<!-- Test 35: Subtracting table means #3 -->
-<conditional name="singtabop" >
-<param name="use_type" value="single" />
-<param name="input" value="examples.5.tsv" />
-<param name="col_row_names" value="has_col_names,has_row_names" />
-<conditional name="user" >
-<param name="mode" value="fulltable" />
-<conditional name="general" >
-<param name="use" value="custom" />
-<param name="fulltable_custom_expr" value="(table.T - table.mean(1)).T" />
-</conditional>
-</conditional>
-</conditional>
-<output name="table" >
-<assert_contents>
-<has_n_columns n="4" />
-<has_line_matching expression="^g1\s+-10\.\d+\s+0\.\d+\s+10\.\d+\s*$" />
-<has_line_matching expression="^g4\s+47\.3\d+\s+-23\.6\d+\s+-23\.6\d+\s*$" />
-</assert_contents>
-</output>
-</test>
-<test expect_num_outputs="1" >
-<!-- Test 36: Negative range test #1 -->
 <expand macro="test_inputs_ranges" >
 <param name="select_cols_wanted" value="-2:2,1,-1" />
 <param name="select_rows_wanted" value="1,3:-3,1" />
 </expand>
 <output name="table" >
 <has_line_matching expression="^g1\s+20\s+30\s+10\s+20\s+10\s+30$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 37: Negative range test #2 -->
+<!-- Test 35: Negative range test #2 -->
 <expand macro="test_inputs_ranges" >
 <param name="select_cols_wanted" value="-1,-3,3:-3,2" />
 <param name="select_rows_wanted" value="3:-1" />
 <param name="select_keepdupe" value="" />
 </expand>
 <has_line_matching expression="^g4\s+3\s+81\s+3\s+6\s+81\s+6$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1">
-<!-- Test 38: Skip first 3 lines -->
+<!-- Test 36: Skip first 3 lines -->
 <conditional name="singtabop" >
 <param name="use_type" value="single" />
 <param name="input" value="skiplines.tsv" />
 <section name="adv" >
 <param name="header" value="2" />
 <has_line_matching expression="^g4\s+81\s+6\s+3$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1">
-<!-- Test 39: Skip first 3 lines -->
+<!-- Test 37: Skip first 3 lines -->
 <conditional name="singtabop" >
 <param name="use_type" value="single" />
 <param name="input" value="skiplines.tsv" />
 <section name="adv" >
 <param name="header" value="2" />
 <has_line_matching expression="^\s+$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 40: Row Col custom op #1 -->
+<!-- Test 38: Row Col replace with format spec #1 -->
 <conditional name="singtabop" >
 <param name="use_type" value="single" />
 <param name="input" value="examples.1.tsv" />
 <param name="col_row_names" value="has_col_names,has_row_names" />
 <conditional name="user" >
 <param name="mode" value="element" />
 <conditional name="element" >
-<param name="mode" value="custom" />
+<param name="mode" value="replace" />
-<param name="custom_expr" value="&#34;chr%.f&#34; % elem" />
+<param name="replace_value" value="chr{elem:.0f}" />
 </conditional>
 <conditional name="elem_val" >
 <param name="element_op" value="rowcol" />
 <param name="select_cols_wanted" value="2" />
 <param name="select_rows_wanted" value="2,4" />
 <has_line_matching expression="^g4\s+chr81\s+chr6\s+chr3$" />
 </assert_contents>
 </output>
 </test>
 <test expect_num_outputs="1" >
-<!-- Test 41: Row Col custom op #2 -->
+<!-- Test 39: Row Col replace with format spec #2 -->
 <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="element" />
 <conditional name="element" >
-<param name="mode" value="custom" />
+<param name="mode" value="replace" />
-<param name="custom_expr" value="&#34;chr%.f&#34; % elem" />
+<param name="replace_value" value="chr{elem:.0f}" />
 </conditional>
 <conditional name="elem_val" >
 <param name="element_op" value="rowcol" />
 <param name="select_cols_wanted" value="2" />
 <param name="select_rows_wanted" value="2,4" />
 <has_line_matching expression="^g2\s+3\s+chr6\s+9$" />
 <has_line_matching expression="^g4\s+81\s+chr6\s+3$" />
 </assert_contents>
 </output>
 </test>
+<test expect_num_outputs="1">
+<!-- Test 40: Test safety of Replacement value free text
+Tries to escape/reenter config file quoting.
+If the test fails, this shows that Python has performed
+string concatenation upon importing the config file. -->
+<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="element" />
+<conditional name="elem_val">
+<param name="element_op" value="None" />
+</conditional>
+<conditional name="element" >
+<param name="mode" value="replace" />
+<param name="scale_op" value="mod" />
+<param name="replace_value" value="a'+'b" />
+</conditional>
+</conditional>
+</conditional>
+<output name="table" >
+<assert_contents>
+<has_n_columns n="4" />
+<not_has_text text="g1&#009;ab" />
+<not_has_text text="g2&#009;ab" />
+<not_has_text text="g3&#009;ab" />
+<not_has_text text="g4&#009;ab" />
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1" expect_failure="true">
+<!-- Test 41: Test safety of custom expression free text
+Tries to escape/reenter config file quoting.
+This test is expected to fail if either
+- a validator disallows the use of single quotes or
+- the single quotes get sanitized (which is unlikely to result in a
+valid expression); note that in this situation, it cannot be
+guaranteed that the single quote sanitization is safe with
+*every* input
+If the test succeeds unexpectedly, this shows that Python
+has performed string concatenation upon importing the config file
+resulting in each element of the test table being retained.
+-->
+<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="el'+'em" />
+</conditional>
+<conditional name="elem_val" >
+<param name="element_op" value="All" />
+</conditional>
+</conditional>
+</conditional>
+</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
+.. class:: infomark
-chaining successive runs of this tool. This is to provide a more transparent workflow for complex operations.
+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
 ========
 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)))
+.. class:: infomark
+Complex operations (like ones that would benefit from specifying nested
+attributes) can often be broken into subsequent runs ot the tool, in
+which the first run generates an intermediate table representing the result
+of the "inner" operation that the second run can then use as input to
+perform the "outer" operation.
 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.
 * *Column names on first row?* → **Yes**
 * *Row names on first column?* → **Yes**
 * *Type of table operation* →  **Manipulate selected table elements**
-* *Operation to perform* → **Custom**
+* *Operation to perform* → **Replace values**
-* *Custom Expression* → ::
+* *Replacement value* → ::
-"chr%.f" % elem
+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
+`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"

Mercurial > repos > iuc > table_compute

comparison table_compute.xml @ 2:fd9f92324423 draft