annotate awklike-filter.xml @ 0:20e8be1464f5 draft default tip

"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"

<tool id="csvtk_awklike_filter" name="csvtk-advanced-filter" version="@VERSION@+@GALAXY_VERSION@">
    <description> rows by awk-like artithmetic/string expressions</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_cmd" />
    <command detect_errors="exit_code"><![CDATA[

###################
## Start Command ##
###################
csvtk filter2 --num-cpus "\${GALAXY_SLOTS:-1}"

    ## Add additional flags as specified ##
    #######################################
    $global_param.illegal_rows
    $global_param.empty_rows
    $global_param.header
    $global_param.lazy_quotes

    ## Set Tabular input/output flag if first input is tabular ##
    #############################################################
    #if $in_1.is_of_type("tabular"):
        -t -T
    #end if

    ## Set input files ##
    #####################
    $in_1

    ## Specify fields to filter ##
    ##############################
    -f '$in_text'

    ## Specific inputs ##
    #####################
    $line_number
    
    ## To output ##
    ###############
    > filtered

    ]]></command>
    <inputs>
        <expand macro="singular_input"/>
        <param name="in_text" type="text"
            optional="false"
            argument="-f"
            label="Awk-like artithmetic/string expression">
            <help>
                <![CDATA[
        Examples:
        - '$age>12'
        - '$1 > $3'
        - '$name=="abc"'
        - '$1 % 2 == 0'
        More info is available in the help section below. The ' character is invalid and will be replaced, thus you must
        surround strings with double quotes ("string") instead.
            ]]>
            </help>
            <expand macro="text_sanitizer" />
        </param>
        <param name="line_number" type="boolean"
            checked="false"
            truevalue="-n"
            falsevalue=""
            argument="-n"
            label="Print initial line number as the first column"
        />
        <expand macro="global_parameters" />
    </inputs>
    <outputs>
        <data format_source="in_1" from_work_dir="filtered" name="filtered" label="${in_1.name} filtered by ${in_text}" />
    </outputs>
    <tests>
        <test>
            <param name="in_1" value="frequency.tsv" />
            <param name="in_text" value="$3>1" />
            <output name="filtered" file="filtered.tsv" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
    
Csvtk - Filter2 Help
--------------------

Info
####

Csvtk advanced filter (also called filter2) outputs rows that satisfy the input awk-like artithmetic/string expressions. Please see the
`documentation <https://github.com/Knetic/govaluate/blob/master/MANUAL.md>`_ for further details and examples on how to write expressions.

.. class:: warningmark

    Single quotes are not allowed in text inputs!

.. class:: note

    If your wanted column header has a space in it, use the column number. Example: Use $1 if column #1 is called "Colony Counts"

Supported operators and types:

    - Modifiers: + - / * & | ^ ** % >> <<
    - Comparators: > >= < <= == != =~ !~
    - Logical ops: || &&
    - Numeric constants, as 64-bit floating point (12345.678)
    - String constants (double quotes: "foobar")
    - Date constants (double quotes)
    - Boolean constants: true false
    - Parenthesis to control order of evaluation ( )
    - Arrays (anything separated by , within parenthesis: (1, 2, "foo"))
    - Prefixes: ! - ~
    - Ternary conditional: ? :
    - Null coalescence: ??

----

@HELP_INPUT_DATA@


Usage
#####

**Ex. Filter2 on one column:**

Suppose we had the following table:

+---------------+------------+----------+
| Culture Label | Cell Count | Dilution |
+===============+============+==========+
| ECo-1         | 2523       | 1000     |
+---------------+------------+----------+
| LPn-1         | 100        | 1000000  |
+---------------+------------+----------+
| LPn-2         | 4          | 1000     |
+---------------+------------+----------+

If we wanted to find all samples with the label LPn, we could use the filter expression '$1 =~ "LPn*"' to get the following output:

+---------------+------------+----------+
| Culture Label | Cell Count | Dilution |
+===============+============+==========+
| LPn-1         | 100        | 1000000  |
+---------------+------------+----------+
| LPn-2         | 4          | 1000     |
+---------------+------------+----------+

Note how $1 was used to get column 1 due to it containing a space

----

**Ex2. Filter2 with multiple inputs:**

Same input table

+---------------+------------+----------+
| Culture Label | Cell Count | Dilution |
+===============+============+==========+
| ECo-1         | 2523       | 1000     |
+---------------+------------+----------+
| LPn-1         | 100        | 1000000  |
+---------------+------------+----------+
| LPn-2         | 4          | 1000     |
+---------------+------------+----------+

Now if we use the expression '$1 =~ "LPn*" && $Dilution > 1000' to filter on, we would pull out the only row that satisfies both conditions:

+---------------+------------+----------+
| Culture Label | Cell Count | Dilution |
+===============+============+==========+
| LPn-1         | 100        | 1000000  |
+---------------+------------+----------+

----

@HELP_COLUMNS@


@HELP_END_STATEMENT@


    ]]></help>
    <expand macro="citations" />
</tool>