<tool id="Convert characters1" name="Convert"  version="1.0.1">
    <description>delimiters to TAB</description>
    <requirements>
        <requirement type="package" version="3.8">python</requirement>
    </requirements>
    <command>
        python '$__tool_directory__/convert_characters.py'
            '${input}'
            '${convert_from}'
            '${out_file1}'
    </command>
    <inputs>
        <param name="convert_from" type="select" label="Convert all">
            <option value="s">Whitespaces</option>
            <option value="T">Tabs</option>
            <!--<option value="Sp">Spaces</option>-->
            <option value="Dt">Dots</option>
            <option value="C">Commas</option>
            <option value="D">Dashes</option>
            <option value="U">Underscores</option>
            <option value="P">Pipes</option>
            <option value="Co">Colons</option>
        </param>
        <param format="txt" name="input" type="data" label="in Query"/>
    </inputs>
    <outputs>
        <data format="tabular" name="out_file1" />
    </outputs>
    <tests>
        <test>
            <param name="convert_from" value="s"/>
            <param name="input" value="1.bed"/>
            <output name="out_file1" file="eq-convert.dat"/>
        </test>
        <test>
            <param name="convert_from" value="s"/>
            <param name="input" value="a.txt"/>
            <output name="out_file1" file="a.tab"/>
        </test>
    </tests>
    <help>

**What it does**

Converts all delimiters of a specified type into TABs.  Consecutive characters are condensed. For example, if columns are separated by 5 spaces they will converted into 1 tab.

-----

**Example**

- Input file::

    chrX||151283558|151283724|NM_000808_exon_8_0_chrX_151283559_r|0|-
    chrX|151370273|151370486|NM_000808_exon_9_0_chrX_151370274_r|0|-
    chrX|151559494|151559583|NM_018558_exon_1_0_chrX_151559495_f|0|+
    chrX|151564643|151564711|NM_018558_exon_2_0_chrX_151564644_f||||0|+

- Converting all pipe delimiters of the above file to TABs will get::

    chrX  151283558  151283724  NM_000808_exon_8_0_chrX_151283559_r  0  -
    chrX  151370273  151370486  NM_000808_exon_9_0_chrX_151370274_r  0  -
    chrX  151559494  151559583  NM_018558_exon_1_0_chrX_151559495_f  0  +
    chrX  151564643  151564711  NM_018558_exon_2_0_chrX_151564644_f  0  +

    </help>
</tool>