annotate convert.xml @ 0:2c55b0752ea7 draft default tip

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

<tool id="csvtk_convert" name="csvtk-convert" version="@VERSION@+@GALAXY_VERSION@">
    <description> csv to tab or tab to csv</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_cmd" />
    <command detect_errors="exit_code"><![CDATA[

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

#if $in_1.is_of_type("tabular"):
    csvtk tab2csv --num-cpus "\${GALAXY_SLOTS:-1}"

#else:
    csvtk csv2tab --num-cpus "\${GALAXY_SLOTS:-1}"

#end if

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

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

    ## To output ##
    ###############
    #if $in_1.is_of_type("tabular")
        > converted.csv

    #else:
        > converted.tsv

    #end if

    ]]></command>
    <inputs>
        <expand macro="singular_input" />
        <expand macro="global_parameters" />
    </inputs>
    <outputs>
        <data auto_format="true" name="converted" from_work_dir="converted*" label="${in_1.name} converted" />
    </outputs>
    <tests>
        <test>
            <param name="in_1" value="XY_with_break.tabular" />
            <section name="global_param">
                <param name="empty_rows" value="true" />
            </section>
            <output name="converted" file="XY_converted.csv" />
        </test>
        <test>
            <param name="in_1" value="XY_with_break.csv" />
            <section name="global_param">
                <param name="empty_rows" value="true" />
            </section>
            <output name="converted" file="XY_converted.tsv" />
        </test>
    </tests>
    <help><![CDATA[
    
Csvtk - Convert Help
--------------------

Info
####

Csvtk convert converts csv files to tsv files and vice versa. 

.. class:: note

    Output CSV data may not be autodetected properly to CSV format and you may have to manually change the format after.


@HELP_INPUT_DATA@


Usage
#####

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

----

@HELP_COLUMNS@


@HELP_END_STATEMENT@


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