comparison table_compute.xml @ 2:02c3e335a695 draft

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

1:dddadbbac949

<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="@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>
            <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" />
                <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>

  "user_mode": '$singtabop.use_type',
  "outtable": '$table'
}

#if str($singtabop.use_type) == "single":
Data = {
    "tables": [
        {
          "file": '$singtabop.input',
        #if $singtabop.adv.header:

          "nrows": None,
        #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 $singtabop.user.select_cols_wanted:
        "select_cols_wanted": '$singtabop.user.select_cols_wanted',
      #else

        "select_rows_wanted": '$singtabop.user.select_rows_wanted',
      #else
        "select_rows_wanted": None,
      #end if
    }
    #elif $singtabop.user.mode.value == 'filtersumval':
        "filtersumval_mode": '$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,

        "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": 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" : '$singtabop.user.elem_val.element_value',
      #end if
        "element_mode": '$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

            "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}',

                        </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>

                                <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>

                    <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" />

                    <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" />

                </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" >

                    <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" >

                    <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" >

                    <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" >

                    <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" >

                    <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" >

                    <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" />

                    <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">

                    <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" >

                    <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" >

                    <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>

                    <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" />

                    <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" />

                    <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" />

                    <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" />

                    <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.

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)))

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**

     * *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"

2:02c3e335a695

<tool id="table_compute" name="Table Compute" version="@VERSION@">
    <description>computes operations on table data</description>
    <macros>
        <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>
            <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" />
                <conditional name="elem_val">
                    <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": '$op_mode',
    #if $op_mode == 'precision':
        ## Literally do nothing, the user just sets the precision slider
        ## at the top default level
    }
    #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 $op_mode == 'filtersumval':
      #set $filter_type = str($singtabop.user.filtersumval_mode.use)
        "filtersumval_mode": '$filter_type',
        "filtersumval_axis": $singtabop.user.axis,
      #if $filter_type == 'operation':
        "filtersumval_compare": '$singtabop.user.filtersumval_mode.compare_op',
        "filtersumval_op": '$singtabop.user.filtersumval_mode.operation',
        "filtersumval_against": $singtabop.user.filtersumval_mode.against,
        "filtersumval_minmatch": None,
      #elif $filter_type == 'element':
        "filtersumval_compare": None,
        "filtersumval_op": '$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 $op_mode == 'matrixapply':
        "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 $op_mode == 'element':
      #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 $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": $singtabop.user.elem_val.inclusive_selection,
      #else:
        "element_op": '$filter_type',
        ## Value is string or float, parsed in code later
        "element_value" : '$singtabop.user.elem_val.element_value',
      #end if
        "element_mode": '$element_mode',
      #if $element_mode == "replace":
        "element_replace": '$singtabop.user.element.replace_value',
      #elif $element_mode == "modify":
        "element_modify_op": '$singtabop.user.element.modify_op',
      #elif $element_mode == "scale":
        "element_scale_op": '$singtabop.user.element.scale_op',
        "element_scale_value": $singtabop.user.element.scale_value,
      #elif $element_mode == "custom":
        #set $custom_func = str($singtabop.user.element.custom_expr).strip()
        "element_customop": '$custom_func',
      #end if
    }
    #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).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="transpose">Transpose</option>
                                <option value="melt">Melt</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="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: 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 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 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 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 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 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 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 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 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 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 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 34: 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 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 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 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 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="replace" />
                        <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 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="replace" />
                        <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.

.. class:: infomark

    Only a single operation can be performed on the data. Multiple operations
    can be performed by chaining successive runs of this tool. This is to
    provide a more transparent workflow for complex operations.



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* → **Replace values**

     * *Replacement value* → ::

         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"