annotate tabix.xml @ 7:62ce37b4c6e1 draft default tip

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author nilesh
date Wed, 10 Jul 2013 17:20:54 -0400
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1 <tool id="tabix" name="tabix" version="0.0.1">
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2 <description>Generic indexer for TAB-delimited genome position files.</description>
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3 <requirements>
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4 <requirement type="package" version= "0.2.6">tabix</requirement>
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5 </requirements>
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6 <command>
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7 tabix
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8 #if str($position) == "no"
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9 -0
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10 #end if
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11
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12 #if str($options.extension) == "tabular"
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13 #if str($options.columnseq) != ""
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14 -s $options.columnseq
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15 #end if
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16
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17 #if str($options.columnstart) != ""
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18 -b $options.columnstart
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19 #end if
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20
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21 #if str($options.columnend) != ""
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22 -e $options.columnend
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23 #end if
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24
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25 #if str($options.skiplines) != ""
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26 -S $options.skiplines
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27 #end if
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28
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29 #if str($options.skipchar) != ""
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30 -c $options.skipchar
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31 #end if
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32 #else
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33 -p
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34 #end if
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35
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36 $input $region
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37
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38 </command>
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39 <inputs>
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40 <param name="input" type="data" label="Input file" format="gff,bed,sam,vcf,tabular">
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41 </param>
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42 <param name="region" type="text" optional="true" label="Regions (seperate with spaces)"> </param>
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43 <conditional name="optional">
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44 <param name= "extension" type="select" value= "tabular" label= "Input Extension">
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45 <option value="tabular">tabular</option>
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46 <option value="gff">gff</option>
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47 <option value="bed">bed</option>
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48 <option value="sam">sam</option>
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49 <option value="vcf">vcf</option>
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50 </param>
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51 <when value="tabular">
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52 <param name="columnseq" type="integer" optional= "true" label="Column of sequence name" />
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53 <param name="columnstart" type="integer" optional= "true" label="Column of start chromosomal position" />
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54 <param name="columnend" type="integer" optional= "true" label="Column of end chromosomal position" />
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55 <param name="skiplines" type="integer" optional= "true" label="Skip first INT lines" />
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56 <param name="skipchar" type="text" optional= "true" label="Skip lines started with CHAR" />
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57 <param name="position" type= "select" value= "yes" label="1-based? (if not, 0-based)">
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58 <option value= "yes">yes</option>
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59 <option value= "no">no</option>
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60 </param>
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61 </when>
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62 </conditional>
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63 </inputs>
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64
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65 <outputs>
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66 <data format="tabular" name="output" from_work_dir="${input.file_name}.tbi"/>
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67 </outputs>
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68
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69 <help>
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70 **What it does:**
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71
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72 Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
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73
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74 **Citation:**
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75
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76 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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77
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78 http://samtools.sourceforge.net/tabix.shtml
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79
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80 **Example:**
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81
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82 (grep ^"#" in.gff; grep -v ^"#" in.gff | sort -k1,1 -k4,4n) | bgzip > sorted.gff.gz;
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83
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84 tabix -p gff sorted.gff.gz;
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85
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86 tabix sorted.gff.gz chr1:10,000,000-20,000,000;
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87
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88 </help>
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89 </tool>