table_compute: table_compute.xml comparison

comparison table_compute.xml @ 1:9190f11e46cd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute commit 6820ec9431a22576f3716c40feeb27f0b8cf5e83"

author	iuc
date	Fri, 30 Aug 2019 05:27:52 -0400
parents	b38b271a94aa
children	fd9f92324423

comparison

equal deleted inserted replaced

-:b38b271a94aa
+:9190f11e46cd
 <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="@VERSION@">0.9.1</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_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>
+<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" >
 <param name="use_type" value="single" />
 <param name="input" value="small.tsv" />
 <conditional name="user" >
+<yield />
+</conditional>
+</conditional>
+</macro>
+<macro name="test_inputs_ranges" >
+<conditional name="singtabop" >
+<param name="use_type" value="single" />
+<param name="input" value="examples.1.tsv" />
+<conditional name="user" >
+<param name="mode" value="select" />
 <yield />
 </conditional>
 </conditional>
 </macro>
 <!-- macro for umi to transcript tests -->
 </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">
+label="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>
+<option value="has_row_names" selected="true">Row names on the first column</option>
 </param>
+<section name="adv" title="Advanced File Options " expanded="false" >
+<param name="header" type="integer" min="0" optional="true" label="Header begins at line N" help="All lines before line N will be skipped. If a value is set, this will override the above 'Column names on the first row' parameter." />
+<param name="nrows" type="integer" min="0" optional="true" label="Read N lines only" help="Parses only N lines after the header line." />
+<param name="skipfooter" type="integer" min="0" optional="true" label="Skip N lines from bottom" help="Do not use this in conjunction with the 'Read N lines only' parameter." />
+<param name="skip_blank_lines" type="boolean" checked="true" falsevalue="False" truevalue="True" label="Skip blank lines" help="Otherwise it will insert NaN values for every blank line detected." />
+</section>
 </macro>
 <!-- element value macro -->
-<macro name="elem_val_macro" >
+<macro name="elem_val_macro" token_when="@WHEN@" >
-<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" />
+<when value="@WHEN@" >
+<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" />
+</when>
+</macro>
+<!-- Row/Col macro -->
+<macro name="select_rowcols" >
+<param name="select_cols_wanted" type="text" optional="true" label="List of columns to select" help="Comma separated. (e.g. @COPEN@3:5,10,-1,2:-2@CCLOSE@ will select columns @COPEN@3,4,5,10,-1,2,1,0,-1,-2@CCLOSE@, where negative indices refer to the offset from the last index). 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>
 </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 '$__tool_directory__/scripts/table_compute.py' --version
+python '$__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
 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,
 #if str($singtabop.use_type) == "single":
 Data = {
 "tables": [
 {
-"reader_file": '$singtabop.input',
+"file": '$singtabop.input',
-#if 'has_col_names' in str($singtabop.col_row_names):
+#if $singtabop.adv.header:
-"reader_header": 0,
+"header": int('$singtabop.adv.header'),
+#elif 'has_col_names' in str($singtabop.col_row_names):
+"header": 0,
 #else:
-"reader_header": None,
+"header": None,
 #end if
-#if 'has_row_names' in str($singtabop.col_row_names):
+"row_names": #if ('has_row_names' in str($singtabop.col_row_names)) then 0 else False#,
-"reader_row_col": 0,
+"skipfooter": #if $singtabop.adv.skipfooter then int($singtabop.adv.skipfooter) else 0#,
-#else:
+#if $singtabop.adv.skip_blank_lines
-"reader_row_col": False,
+"skip_blank_lines": $singtabop.adv.skip_blank_lines,
+#else
+"skip_blank_lines": None,
+#end if
+#if $singtabop.adv.nrows
+"nrows": int('$singtabop.adv.nrows'),
+#else
+"nrows": None,
 #end if
 }
 ],
 "params": {
 "user_mode_single": '$singtabop.user.mode.value',
 }
 #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)),
+"select_cols_wanted": '$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)),
+"select_rows_wanted": '$singtabop.user.select_rows_wanted',
 #else
 "select_rows_wanted": None,
 #end if
 }
 #elif $singtabop.user.mode.value == 'filtersumval':
 "matrixapply_custom_func": None,
 "matrixapply_op": '$singtabop.user.matrixapply_func.vector_op',
 #end if
 }
 #elif $singtabop.user.mode.value == 'element':
-#if str($singtabop.user.elem_val.element_op) != "None":
+#if str($singtabop.user.elem_val.element_op) == "None":
+"element_op": None,
+#elif str($singtabop.user.elem_val.element_op) == "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',
 ## 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":
 Data = {
 "tables": [
 #for $i, $s in enumerate($singtabop.tables)
 {
 "file": '${s.input}',
-#if 'has_col_names' in str($s.col_row_names):
+#if $s.adv.header:
+"header": int('${s.adv.header}'),
+#elif '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": #if ('has_row_names' in str($s.col_row_names)) then 0 else False#,
-"row_names": 0,
+"skipfooter": #if $s.adv.skipfooter then int('$s.adv.skipfooter') else 0#,
-#else:
+#if $s.adv.skip_blank_lines:
-"row_names": False,
+"skip_blank_lines": $s.adv.skip_blank_lines,
+#else
+"skip_blank_lines": None,
 #end if
+#if $s.adv.nrows:
+"nrows": int('${s.adv.nrows}'),
+#else
+"nrows": None,
+#end if
 },
 #end for
 ],
 'params': {
 "fulltable_customop" : '$custom_func',
 <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="select_rowcols" />
-<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>
 <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"
+<param name="custom_expr" type="text" label="Custom expression on 'elem'"
-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.">
-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>
+<option value="rowcol" >Specific Rows and/or Columns</option>
 </expand>
 </param>
 <when value="None" />
-<when value="lt">
+<expand macro="elem_val_macro" when="lt" />
-<expand macro="elem_val_macro" />
+<expand macro="elem_val_macro" when="le" />
-</when>
+<expand macro="elem_val_macro" when="gt" />
-<when value="le">
+<expand macro="elem_val_macro" when="ge" />
-<expand macro="elem_val_macro" />
+<expand macro="elem_val_macro" when="eq" />
-</when>
+<expand macro="elem_val_macro" when="ne" />
-<when value="gt">
+<when value="rowcol" >
-<expand macro="elem_val_macro" />
+<expand macro="select_rowcols" />
-</when>
+<param name="inclusive_selection" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Inclusive Selection" help="If enabled, all elements that match ANY row or column given above will be acted on. Otherwise, only the elements that match BOTH a row or column given above will be acted on." />
-<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>
 <has_line_matching expression="^one\s+1\s+2\s+3$" />
 <has_line_matching expression="^two\s+4\s+5\s+6$" />
 </assert_contents>
 </output>
 </test>
+<test expect_num_outputs="1" >
+<!-- Test 33: Subtracting table means #1 -->
+<conditional name="singtabop" >
+<param name="use_type" value="single" />
+<param name="input" value="examples.5.tsv" />
+<param name="col_row_names" value="has_col_names,has_row_names" />
+<conditional name="user" >
+<param name="mode" value="fulltable" />
+<conditional name="general" >
+<param name="use" value="custom" />
+<param name="fulltable_custom_expr" value="table - table.mean(1)/table.std(1)" />
+</conditional>
+</conditional>
+</conditional>
+<output name="table" >
+<assert_contents>
+<has_n_columns n="8" />
+<!-- should give nonsense empty output -->
+<has_line_matching expression="^\sc1\sc2\sc3\sg1\sg2\sg3\sg4$" />
+<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*$" />
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1" >
+<!-- Test 36: Negative range test #1 -->
+<expand macro="test_inputs_ranges" >
+<param name="select_cols_wanted" value="-2:2,1,-1" />
+<param name="select_rows_wanted" value="1,3:-3,1" />
+</expand>
+<output name="table" >
+<assert_contents>
+<has_n_columns n="7" />
+<has_line_matching expression="^\s*c2\s+c3\s+c1\s+c2\s+c1\s+c3$" />
+<has_line_matching expression="^g1\s+20\s+30\s+10\s+20\s+10\s+30$" />
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1" >
+<!-- Test 37: Negative range test #2 -->
+<expand macro="test_inputs_ranges" >
+<param name="select_cols_wanted" value="-1,-3,3:-3,2" />
+<param name="select_rows_wanted" value="3:-1" />
+<param name="select_keepdupe" value="" />
+</expand>
+<output name="table" >
+<assert_contents>
+<has_n_columns n="7" />
+<has_line_matching expression="^\s*c3\s+c1\s+c3\s+c2\s+c1\s+c2$" />
+<has_line_matching expression="^g4\s+3\s+81\s+3\s+6\s+81\s+6$" />
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- Test 38: Skip first 3 lines -->
+<conditional name="singtabop" >
+<param name="use_type" value="single" />
+<param name="input" value="skiplines.tsv" />
+<section name="adv" >
+<param name="header" value="2" />
+<param name="nrows" value="4" />
+<param name="skip_blank_lines" value="true" />
+</section>
+<conditional name="user" >
+<param name="mode" value="precision" />
+</conditional>
+</conditional>
+<param name="precision" value="2" />
+<output name="table" >
+<assert_contents>
+<has_n_columns n="4" />
+<has_line_matching expression="^\s+c1\s+c2\s+c3$" />
+<has_line_matching expression="^g4\s+81\s+6\s+3$" />
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1">
+<!-- Test 39: Skip first 3 lines -->
+<conditional name="singtabop" >
+<param name="use_type" value="single" />
+<param name="input" value="skiplines.tsv" />
+<section name="adv" >
+<param name="header" value="2" />
+<param name="skipfooter" value="2" />
+<param name="skip_blank_lines" value="false" />
+</section>
+<conditional name="user" >
+<param name="mode" value="precision" />
+</conditional>
+</conditional>
+<param name="precision" value="2" />
+<param name="out_opts" value="" />
+<output name="table" >
+<assert_contents>
+<has_n_columns n="3" />
+<has_line_matching expression="^10.00\s+20.00\s+30.00$" />
+<has_line_matching expression="^\s+$" />
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1" >
+<!-- Test 40: Row Col custom op #1 -->
+<conditional name="singtabop" >
+<param name="use_type" value="single" />
+<param name="input" value="examples.1.tsv" />
+<param name="col_row_names" value="has_col_names,has_row_names" />
+<conditional name="user" >
+<param name="mode" value="element" />
+<conditional name="element" >
+<param name="mode" value="custom" />
+<param name="custom_expr" value="&#34;chr%.f&#34; % elem" />
+</conditional>
+<conditional name="elem_val" >
+<param name="element_op" value="rowcol" />
+<param name="select_cols_wanted" value="2" />
+<param name="select_rows_wanted" value="2,4" />
+<param name="inclusive_selection" value="True" />
+</conditional>
+</conditional>
+</conditional>
+<output name="table" >
+<assert_contents>
+<has_n_columns n="4" />
+<has_line_matching expression="^g2\s+chr3\s+chr6\s+chr9$" />
+<has_line_matching expression="^g4\s+chr81\s+chr6\s+chr3$" />
+</assert_contents>
+</output>
+</test>
+<test expect_num_outputs="1" >
+<!-- Test 41: Row Col custom op #2 -->
+<conditional name="singtabop" >
+<param name="use_type" value="single" />
+<param name="input" value="examples.1.tsv" />
+<param name="col_row_names" value="has_col_names,has_row_names" />
+<conditional name="user" >
+<param name="mode" value="element" />
+<conditional name="element" >
+<param name="mode" value="custom" />
+<param name="custom_expr" value="&#34;chr%.f&#34; % elem" />
+</conditional>
+<conditional name="elem_val" >
+<param name="element_op" value="rowcol" />
+<param name="select_cols_wanted" value="2" />
+<param name="select_rows_wanted" value="2,4" />
+<param name="inclusive_selection" value="False" />
+</conditional>
+</conditional>
+</conditional>
+<output name="table" >
+<assert_contents>
+<has_n_columns n="4" />
+<has_line_matching expression="^g2\s+3\s+chr6\s+9$" />
+<has_line_matching expression="^g4\s+81\s+chr6\s+3$" />
+</assert_contents>
+</output>
+</test>
 </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.
 * *Column* → "bar"
 * *Values* → "baz"
 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
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+We have the following table
+=== === === ===
+.  c1  c2  c3
+=== === === ===
+g1  10  20  30
+g2   3   3   9
+g3   4   8  12
+g4  81   6   3
+=== === === ===
+and we want to add "chr" to the elements in column 2 AND rows 2 and 4:
+=== === ==== ===
+.  c1    c2  c3
+=== === ==== ===
+g1  10    20  30
+g2   3  chr3   9
+g3   4     8  12
+g4  81  chr6   3
+=== === ==== ===
+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* → ::
+"chr%.f" % elem
+* *Operate on elements* → **Specific Rows and/or Columns**
+* *List of columns to select* → "2"
+* *List of rows to select* → "2,4"
+* *Inclusive Selection* → "No"
+If we wanted to instead add "chr" to the ALL elements in column 2 and rows 2 and 4, we would repeat the steps above but set the *Inclusive Selection* to "Yes", to give:
+=== =====  ===== =====
+.    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 @ 1:9190f11e46cd draft