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1 <tool id="bgzip" name="bgzip" version="0.0.1">
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2 <description>Block compression/decompression utility. Required for use of tabix.</description>
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3 <requirements>
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4 <requirements type="package" version="0.2.6">tabix</requirements>
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5 </requirements>
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6 <command>
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7 bgzip
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8
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9 #if str($virtualOffset) != ""
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10 -b $virtualOffset
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11 #end if
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12
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13 #if str($size) != ""
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14 -s $size
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15 #end if
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16
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17 $input
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18 </command>
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19 <inputs>
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20 <param name="input" type="data" label="Input file" />
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21 <param name="virtualOffset" type="text" optional="yes" label="Virtual Offset" />
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22 <param name="size" type="text" optional="yes" label="Size" />
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23 </inputs>
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24
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25 <outputs>
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26 <data format= "bgz" name="output" from_work_dir="${input.file_name}.bgz"/>
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27 </outputs>
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28
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29 <help>
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30 **What it does:**
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31
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32 The input data file is sorted and compressed by bgzip which has a gzip(1) like interface. Tabix requires the file to be compressed using this tool first.
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33
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34 **Citation:**
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35
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36 Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.
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37
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38 http://samtools.sourceforge.net/tabix.shtml
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39
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40 **Example:**
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41
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42 (grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
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43
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44 tabix -p gff sorted.gff.gz;
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45
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46 tabix sorted.gff.gz chr1:10,000,000-20,000,000;
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47
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48 </help>
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49 </tool>
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