annotate filter.xml @ 0:58ed60d20336 draft default tip

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

<tool id="csvtk_filter" name="csvtk-filter" version="@VERSION@+@GALAXY_VERSION@">
    <description> rows through arithmetic expression(s)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_cmd" />
    <command detect_errors="exit_code"><![CDATA[

###################
## Start Command ##
###################
csvtk filter --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 -f '$in_text'

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

    ]]></command>
    <inputs>
        <expand macro="singular_input"/>
        <param name="in_text" type="text"
            optional="false"
            argument="-F -f"
            label="Specify column(s) and numeric expression to filter for"
            help="Give column name/number and the numeric expression that you want to evaluate. Example: 'frequency>4'. See help below for more examples">
            <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"
        />
        <param name="any" type="boolean"
            checked="false"
            truevalue="--any"
            falsevalue=""
            argument="--any"
            label="Return row if any row value satisfies the condition"
            help="For multiple column filters only"
        />
        <expand macro="global_parameters" />
    </inputs>
    <outputs>
        <data format_source="in_1" from_work_dir="filtered" name="filtered" label="${in_1.name} filtered with ${in_text}" />
    </outputs>
    <tests>
        <test>
            <param name="in_1" value="frequency.tsv" />
            <param name="in_text" value="frequency>1" />
            <output name="filtered" file="filtered.tsv" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
    
Csvtk - Filter Help
-------------------

Info
####

Csvtk filter outputs rows that satisfy an input numerical expression on the specified column(s).

.. class:: warningmark

    Single quotes are not allowed in text inputs!

@HELP_INPUT_DATA@


Usage
#####

**Ex. Filter 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 used the filter expression "Cell Count>100", we would get the following output column:

+---------------+------------+----------+
| Culture Label | Cell Count | Dilution |
+===============+============+==========+
| ECo-1         | 2523       | 1000     |
+---------------+------------+----------+

----

**Ex2. Filter on two columns:**

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 "2-3>50" to filter on, we would pull out:

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

Row 3 is not returned back as its column 2 is not greater than 50. 

However, if **Any** is set to Yes, then Row 3 would be returned as its column 3 is greater than 50
making it satisfy one part of the expression.


**Note:** - Multiple columns can only be specified with a "-"

----

@HELP_COLUMNS@


@HELP_END_STATEMENT@


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