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1 <tool id="tabix" name="Tabix" version="1.0.0">
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2 <description>Index tab-delimited file</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 ln -s -f $input tabix_in.${input.ext} &&
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8 tabix -f
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9
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10 #if str( $filetype_cond.filetype ) == "gff":
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11 -p gff
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12 #elif str( $filetype_cond.filetype ) == "bed":
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13 -p bed
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14 #elif str( $filetype_cond.filetype ) == "sam":
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15 -p sam
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16 #elif str( $filetype_cond.filetype ) == "vcf":
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17 -p vcf
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18
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19 #elif str( $input.ext ) == "gff":
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20 -p gff
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21 #elif str( $input.ext ) == "bed":
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22 -p bed
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23 #elif str( $input.ext ) == "sam":
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24 -p sam
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25 #elif str( $input.ext ) == "vcf":
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26 -p vcf
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27 #elif str( $input.ext ) == "vcf_bgzip":
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28 -p vcf
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29 #end if
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30
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31 #if str( $filetype_cond.filetype ) == "other":
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32 #if str( $filetype_cond.seq_name_column ) != "":
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33 -s ${filetype_cond.seq_name_column}
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34 #end if
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35 #if str( $filetype_cond.start_column ) != "":
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36 -b ${filetype_cond.start_column}
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37 #end if
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38 #if str( $filetype_cond.end_column ) != "":
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39 -e ${filetype_cond.end_column}
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40 #end if
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41 #if str( $filetype_cond.skip_first_lines ) != "":
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42 -S ${filetype_cond.skip_first_lines}
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43 #end if
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44 #if str( $filetype_cond.comment_symbol ) != "":
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45 -c "${filetype_cond.comment_symbol}"
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46 #end if
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47 #if str( $filetype_cond.zero_based ) == "true":
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48 -0
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49 #end if
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50 #end if
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51 tabix_in.${input.ext} &&
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52 cp tabix_in.${input.ext}.tbi $output
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53 </command>
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54 <inputs>
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55 <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."/>
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56 <conditional name="filetype_cond">
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57 <param name="filetype" type="select" label="Input filetype" help="-p. Set filetype of input file in case it is not detected properly.">
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58 <option value="none" selected="True">None selected</option>
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59 <option value="gff">GFF</option>
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60 <option value="bed">BED</option>
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61 <option value="sam">SAM</option>
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62 <option value="vcf">VCF</option>
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63 <option value="other">Other</option>
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64 </param>
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65 <when value="other">
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66 <param name="seq_name_column" type="integer" optional="true" label="Sequence name column" help="-s" />
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67 <param name="start_column" type="integer" optional="true" label="Start column" help="-b" />
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68 <param name="end_column" type="integer" optional="true" label="End column" help="-e" />
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69 <param name="skip_first_lines" type="integer" optional="true" label="Skip first n lines" help="-S" />
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70 <param name="comment_symbol" type="text" label="Symbol for comment/meta lines" help="-c">
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71 <sanitizer invalid_char="">
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72 <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid>
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73 </sanitizer>
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74 </param>
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75 <param name="zero_based" type="boolean" checked="False" label="Use zero-based coordinates" help="-0" />
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76 </when>
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77
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78 </conditional>
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79
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80 </inputs>
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81 <outputs>
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82 <data name="output" label="${tool.name} on ${on_string}" />
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83 </outputs>
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84 <help>
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85 **About this tool**
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86
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87 **Tabix**: Generic indexer for TAB-delimited genome position files. Outputs index of input file.
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88
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89 More info here: http://www.htslib.org/doc/tabix.html
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90 </help>
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91 </tool>
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