view sort.xml @ 0:4a1ea249955e draft default tip

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

<tool id="csvtk_sort" name="csvtk-sort" version="@VERSION@+@GALAXY_VERSION@">
    <description> column(s) </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_cmd" />
    <command detect_errors="exit_code"><![CDATA[

###################
## Start Command ##
###################
csvtk sort --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.is_of_type("tabular"):
        -t -T
    #end if

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

    ## Set up Sort Repeats ##
    ##########################
    #for $repeat in $field
        -k '$repeat.column_text.in_text':${repeat.sort.sort_type}${repeat.reverse_order}
    
        #if $repeat.sort.sort_type == 'u'
            -L '$repeat.column_text.in_text':'$repeat.sort.levels_file'
        #end if
    #end for
    
    ## To output ##
    ###############
    > sorted

    ]]></command>
    <inputs>
        <expand macro="singular_input"/>
        <repeat name="field" title="Select Column and Sorting method" min="1" >
            <expand macro="singular_fields_input" />
            <conditional name="sort">
                <param name="sort_type" type="select" label="Sort Type" help="Select how to sort data">
                    <option value="N">Natural</option>
                    <option value="n">Numerical</option>
                    <option value="u">User-Defined (Specify File)</option>
                </param>
                <when value="N" />
                <when value="n" />
                <when value="u" >
                    <param name="levels_file" type="data" format="txt" argument="-L"
                        optional="false"
                        label="User defined levels file"
                        help="If using user defined sorting, specift input text file with one level per line. Example can be found in the help section below."
                    />
                </when>
            </conditional>
            <param name="reverse_order" type="boolean" argument="r" checked="false"
                truevalue="r"
                falsevalue=""
                label="Reverse Sort"
            />
        </repeat>
        <expand macro="ignore_case" />
        <expand macro="global_parameters" />
    </inputs>
    <outputs>
        <data format_source="in_1" from_work_dir="sorted" name="sorted" label="${in_1.name} sorted" />
    </outputs>
    <tests>
        <test>
            <param name="in_1" value="Animals_More.csv" />
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="2" />
                </conditional>
                <conditional name="sort">
                    <param name="sort_type" value="u" />
                    <param name="levels_file" value="sort_order.txt" />
                </conditional>
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="3" />
                </conditional>
                <conditional name="sort">
                    <param name="sort_type" value="n" />
                </conditional>
                <param name="reverse_order" value="true"  />
            </repeat>
            <repeat name="field">
                <conditional name="column_text">
                    <param name="select" value="string" />
                    <param name="in_text" value="1" />
                </conditional>
                <conditional name="sort">
                    <param name="sort_type" value="N" />
                </conditional>
            </repeat>
            <output name="sorted" value="sorted_1.csv" />
        </test>
    </tests>
    <help><![CDATA[
    
Csvtk - Sort Help
-----------------

Info
####

Csvtk-sort sorts columns 


.. class:: warningmark

    Single quotes are not allowed in text inputs!

----


@HELP_INPUT_DATA@


Usage
#####

**Ex. Separate with Dropping Data**



----


@HELP_COLUMNS@


@HELP_END_STATEMENT@


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