<tool id="tabix" name="Tabix" version="1.0.0">
    <description>Index tab-delimited file</description>
    <requirements>
        <requirement type="package" version="0.2.6">tabix</requirement>
    </requirements>
    <command>
        ln -s -f $input tabix_in.${input.ext} &amp;&amp;
        tabix -f

        #if str( $filetype_cond.filetype ) == "gff":
            -p gff
        #elif str( $filetype_cond.filetype ) == "bed":
            -p bed
        #elif str( $filetype_cond.filetype ) == "sam":
            -p sam
        #elif str( $filetype_cond.filetype ) == "vcf":
            -p vcf

        #elif str( $input.ext ) == "gff":
            -p gff
        #elif str( $input.ext ) == "bed":
            -p bed
        #elif str( $input.ext ) == "sam":
            -p sam
        #elif str( $input.ext ) == "vcf":
            -p vcf
        #elif str( $input.ext ) == "vcf_bgzip":
            -p vcf
        #end if

        #if str( $filetype_cond.filetype ) == "other":
            #if str( $filetype_cond.seq_name_column ) != "":
                -s ${filetype_cond.seq_name_column}
            #end if
            #if str( $filetype_cond.start_column ) != "":
                -b ${filetype_cond.start_column}
            #end if
            #if str( $filetype_cond.end_column ) != "":
                -e ${filetype_cond.end_column}
            #end if
            #if str( $filetype_cond.skip_first_lines ) != "":
                -S ${filetype_cond.skip_first_lines}
            #end if
            #if str( $filetype_cond.comment_symbol ) != "":
                -c "${filetype_cond.comment_symbol}"
            #end if
            #if str( $filetype_cond.zero_based ) == "true":
                -0
            #end if
        #end if
        tabix_in.${input.ext} &amp;&amp;
        cp tabix_in.${input.ext}.tbi $output
    </command>
    <inputs>
        <param name="input" type="data" label="Input file" help="File must be bgzip-compressed and tab-delimited. Run Bgzip Galaxy tool if file is not bgzip-compressed."/>
        <conditional name="filetype_cond">
            <param name="filetype" type="select" label="Input filetype" help="-p. Set filetype of input file in case it is not detected properly.">
                <option value="none" selected="True">None selected</option>
                <option value="gff">GFF</option>
                <option value="bed">BED</option>
                <option value="sam">SAM</option>
                <option value="vcf">VCF</option>
                <option value="other">Other</option>
            </param>
            <when value="other">
                <param name="seq_name_column" type="integer" optional="true" label="Sequence name column" help="-s" />
                <param name="start_column" type="integer" optional="true" label="Start column" help="-b" />
                <param name="end_column" type="integer" optional="true" label="End column" help="-e" />
                <param name="skip_first_lines" type="integer" optional="true" label="Skip first n lines" help="-S" />
                <param name="comment_symbol" type="text" label="Symbol for comment/meta lines" help="-c">
                    <sanitizer invalid_char="">
                        <valid initial="string.letters,string.digits"><add value="~`!@#$%^&amp;*()-_=+[{]}\|;:'&quot;,&lt;.&gt;?/ " /> </valid>
                    </sanitizer>
                </param>
                <param name="zero_based" type="boolean" checked="False" label="Use zero-based coordinates" help="-0" />
            </when>

        </conditional>

    </inputs>
    <outputs>
        <data name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <help>
**About this tool**

**Tabix**: Generic indexer for TAB-delimited genome position files. Outputs index of input file.

More info here: http://www.htslib.org/doc/tabix.html
  </help>
</tool>