annotate concat.xml @ 0:cd31fe25d6ac draft default tip

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

<tool id="csvtk_concat" name="csvtk-concatenate" version="@VERSION@+@GALAXY_VERSION@">
    <description> concatenate CSV/TSV files by rows</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_cmd" />
    <command detect_errors="exit_code"><![CDATA[

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

csvtk concat --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 first input is tabular ##
    #############################################################
    #if $in_1[0].is_of_type("tabular"):
        -t -T
    #end if

    ## Set input files ##
    #####################
    #for $file in $in_1:
        '$file'
    #end for
    
    ## Fill unmatched ##
    ####################
    #if $fill.select == 'yes' 
    -u '$fill.fill_value'
    #end if
    
    ## To output ##
    ###############
    > concat

    ]]></command>
    <inputs>
        <expand macro="multi_input" />
        <conditional name="fill">
            <param name="select" type="select" label="Fill unmatched columns?">
                <option value="yes">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes">
                <param name="fill_value" type="text" value="-" argument="-u"
                    optional="false"
                    label="Fill string"
                    help="Input character string that will fill unmatched columns. The ' character is not allowed">
                    <expand macro="text_sanitizer" />
                </param>
            </when>
            <when value="no" />
        </conditional>
        <expand macro="ignore_case" />
        <expand macro="global_parameters" />
    </inputs>
    <outputs>
        <data format_source="in_1" name="concat" from_work_dir="concat" label="${in_1[0].name} concatenated" />
    </outputs>
    <tests>
        <test>
            <param name="in_1" value="test.csv,other.csv,another.csv" />
            <conditional name="fill">
                <param name="select" value="no" />
            </conditional>
            <output name="concat" file="concat_2.csv" />
        </test>
        <test>
            <param name="in_1" value="test.csv,other.csv,another.csv" />
            <output name="concat" file="concat_1.csv" />
        </test>
    </tests>
    <help><![CDATA[
    
Csvtk - Collapse Help
---------------------

Info
####

Csvtk concatenate CSV/TSV files by rows

**Order is important to input and the first file input will determine the header names!**

.. class:: warningmark

    Single quotes are not allowed in text inputs!

@HELP_INPUT_DATA@


Usage
#####

To run csvtk-concatenate, all you need is one or more valid (as defined above) CSV or TSV files (of the same type) to concatenate together.

**Example Concatenate**

::

    If you have the following two files:

    +-------+--------+           +-------+------+
    | Name  | Colour |           | Name  | Food |
    +=======+========+     +     +=======+======+
    | Steve | Blue   |           | Fred  | Eggs |
    +-------+--------+           +-------+------+
                                 | Steve | Ham  |
                                 +-------+------+

    -----------------------------------------------

    They would concatenate to:

    +-------+--------+
    | Name  | Colour |
    +=======+========+
    | Steve | Blue   |
    +-------+--------+
    | Steve |        |
    +-------+--------+

    If you want, you can fill the empty cell with any set of characters so long as it doesn't contain an apostraphe (')

----

@HELP_COLUMNS@


@HELP_END_STATEMENT@


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