|
19
|
1 <tool id="tabix" name="Tabix" version="1.0.0">
|
|
|
2 <description>Index tab-delimited file</description>
|
|
|
3 <command>
|
|
|
4 ln -s -f $input tabix_in.${input.ext} &&
|
|
|
5 tabix -f
|
|
|
6
|
|
|
7 #if str( $filetype_cond.filetype ) == "gff":
|
|
|
8 -p gff
|
|
|
9 #elif str( $filetype_cond.filetype ) == "bed":
|
|
|
10 -p bed
|
|
|
11 #elif str( $filetype_cond.filetype ) == "sam":
|
|
|
12 -p sam
|
|
|
13 #elif str( $filetype_cond.filetype ) == "vcf":
|
|
|
14 -p vcf
|
|
|
15
|
|
|
16 #elif str( $input.ext ) == "gff":
|
|
|
17 -p gff
|
|
|
18 #elif str( $input.ext ) == "bed":
|
|
|
19 -p bed
|
|
|
20 #elif str( $input.ext ) == "sam":
|
|
|
21 -p sam
|
|
|
22 #elif str( $input.ext ) == "vcf":
|
|
|
23 -p vcf
|
|
|
24 #elif str( $input.ext ) == "vcf_bgzip":
|
|
|
25 -p vcf
|
|
|
26 #end if
|
|
|
27
|
|
|
28 #if str( $filetype_cond.filetype ) == "other":
|
|
|
29 #if str( $filetype_cond.seq_name_column ) != "":
|
|
|
30 -s ${filetype_cond.seq_name_column}
|
|
|
31 #end if
|
|
|
32 #if str( $filetype_cond.start_column ) != "":
|
|
|
33 -b ${filetype_cond.start_column}
|
|
|
34 #end if
|
|
|
35 #if str( $filetype_cond.end_column ) != "":
|
|
|
36 -e ${filetype_cond.end_column}
|
|
|
37 #end if
|
|
|
38 #if str( $filetype_cond.skip_first_lines ) != "":
|
|
|
39 -S ${filetype_cond.skip_first_lines}
|
|
|
40 #end if
|
|
|
41 #if str( $filetype_cond.comment_symbol ) != "":
|
|
|
42 -c "${filetype_cond.comment_symbol}"
|
|
|
43 #end if
|
|
|
44 #if str( $filetype_cond.zero_based ) == "true":
|
|
|
45 -0
|
|
|
46 #end if
|
|
|
47 #end if
|
|
|
48 tabix_in.${input.ext} &&
|
|
|
49 cp tabix_in.${input.ext}.tbi $output
|
|
|
50 </command>
|
|
|
51 <inputs>
|
|
|
52 <param name="input" type="data" label="Input file" help="File must be bgzip-compressed and tab-delimited. Run Bgzip Galaxy tool if file is not bgzip-compressed."/>
|
|
|
53 <conditional name="filetype_cond">
|
|
|
54 <param name="filetype" type="select" label="Input filetype" help="-p. Set filetype of input file in case it is not detected properly.">
|
|
|
55 <option value="none" selected="True">None selected</option>
|
|
|
56 <option value="gff">GFF</option>
|
|
|
57 <option value="bed">BED</option>
|
|
|
58 <option value="sam">SAM</option>
|
|
|
59 <option value="vcf">VCF</option>
|
|
|
60 <option value="other">Other</option>
|
|
|
61 </param>
|
|
|
62 <when value="other">
|
|
|
63 <param name="seq_name_column" type="integer" optional="true" label="Sequence name column" help="-s" />
|
|
|
64 <param name="start_column" type="integer" optional="true" label="Start column" help="-b" />
|
|
|
65 <param name="end_column" type="integer" optional="true" label="End column" help="-e" />
|
|
|
66 <param name="skip_first_lines" type="integer" optional="true" label="Skip first n lines" help="-S" />
|
|
|
67 <param name="comment_symbol" type="text" label="Symbol for comment/meta lines" help="-c">
|
|
|
68 <sanitizer invalid_char="">
|
|
|
69 <valid initial="string.letters,string.digits"><add value="~`!@#$%^&*()-_=+[{]}\|;:'",<.>?/ " /> </valid>
|
|
|
70 </sanitizer>
|
|
|
71 </param>
|
|
|
72 <param name="zero_based" type="boolean" checked="False" label="Use zero-based coordinates" help="-0" />
|
|
|
73 </when>
|
|
|
74
|
|
|
75 </conditional>
|
|
|
76
|
|
|
77 </inputs>
|
|
|
78 <outputs>
|
|
|
79 <data name="output" label="${tool.name} on ${on_string}" />
|
|
|
80 </outputs>
|
|
|
81 <help>
|
|
|
82 **About this tool**
|
|
|
83
|
|
|
84 **Tabix**: Generic indexer for TAB-delimited genome position files. Outputs index of input file.
|
|
|
85
|
|
|
86 More info here: http://www.htslib.org/doc/tabix.html
|
|
|
87 </help>
|
|
|
88 </tool>
|
