annotate cut.xml @ 0:5b5330a8dfac draft default tip

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

<tool id="csvtk_cut" name="csvtk-cut" version="@VERSION@+@GALAXY_VERSION@">
    <description> and keep selected columns</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_cmd" />
    <command detect_errors="exit_code"><![CDATA[

###################
## Start Command ##
###################

csvtk cut --num-cpus "\${GALAXY_SLOTS:-1}"

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

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

    ## Set Input ##
    ###############
    '$in_1'

    ## Specify fields for collapse ##
    #################################
    -F -f '$column_text.in_text'

    ## To output ##
    ###############
    > cut

    ]]></command>
    <inputs>
        <expand macro="singular_input" />
        <expand macro="fields_input" />
        <expand macro="ignore_case" />
        <expand macro="global_parameters" />
    </inputs>
    <outputs>
        <data format_source="in_1" name="cut" from_work_dir="cut" label="${in_1.name} cut out column(s) ${column_text.in_text}" />
    </outputs>
    <tests>
        <test>
            <param name="in_1" value="plot.csv" />
            <conditional name="column_text">
                <param name="select" value="column" />
                <param name="in_text" value="2,3" />
            </conditional>
            <output name="cut" file="cut_1.csv" ftype="csv" />
        </test>
        <test>
            <param name="in_1" value="plot.csv" />
            <conditional name="column_text">
                <param name="select" value="string" />
                <param name="in_text" value="-2" />
            </conditional>
            <output name="cut" file="cut_2.csv" ftype="csv" />
        </test>
    </tests>
    <help><![CDATA[
    
Csvtk - Cut Help
----------------

Info
####

Csvtk Cut cuts specified columns to create an output

Csvtk Cut can be used to keep columns with normal inputs such as the column name or number. It
can also be used to specify columns to remove with a "-" at the start. An example can be seen below.

.. class:: warningmark

    Single quotes are not allowed in text inputs!

@HELP_INPUT_DATA@


Usage
#####

To run csvtk-cut, all you need is a valid (as defined above) CSV or TSV file

**Example cut to keep columns**

Input table:

+--------+--------+----------+
| Name   | Colour | Food     |
+========+========+==========+
| Eric   | Blue   | Apples   |
+--------+--------+----------+
| Darian | Blue   | Pancakes |
+--------+--------+----------+
| Daniel | Red    | Apples   |
+--------+--------+----------+
| Emily  | Blue   | Apples   |
+--------+--------+----------+

Now if we wanted to cut out and keep columns 1 and 2, our column input string (-F -f) would be "1,2"
and would result in the following table:

+--------+--------+
| Name   | Colour |
+========+========+
| Eric   | Blue   |
+--------+--------+
| Darian | Blue   |
+--------+--------+
| Daniel | Red    |
+--------+--------+
| Emily  | Blue   |
+--------+--------+

--------

**Example cut to remove column**

Similar input table as above:

+--------+--------+----------+-----------------+
| Name   | Colour | Food     | Unneeded Column |
+========+========+==========+=================+
| Eric   | Blue   | Apples   | fadah           |
+--------+--------+----------+-----------------+
| Darian | Blue   | Pancakes | ewq3rfa         |
+--------+--------+----------+-----------------+
| Daniel | Red    | Apples   | feda356t        |
+--------+--------+----------+-----------------+
| Emily  | Blue   | Apples   | a342qadef       |
+--------+--------+----------+-----------------+

Now, we have a garbage last column and we want to keep everything else. We could input "1,2,3" to keep the first 3 columns, 
OR if we set the input column name to "-4" or "-Unneeded Column" csvtk cut will remove the final column giving the following:

+--------+--------+----------+
| Name   | Colour | Food     |
+========+========+==========+
| Eric   | Blue   | Apples   |
+--------+--------+----------+
| Darian | Blue   | Pancakes |
+--------+--------+----------+
| Daniel | Red    | Apples   |
+--------+--------+----------+
| Emily  | Blue   | Apples   |
+--------+--------+----------+

----

@HELP_COLUMNS@


@HELP_END_STATEMENT@


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