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comparison tabix.xml @ 19:8d9aa0763dc1 draft

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author wrtz
date Thu, 14 Jan 2016 17:51:54 -0500
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18:44265821f01f 19:8d9aa0763dc1
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} &amp;&amp;
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} &amp;&amp;
49 cp tabix_in.${input.ext}.tbi $output
50 </command>
51 <inputs>
52 <param name="input" type="data" label="Input file" help="File must be bgzip-compressed and tab-delimited. Run Bgzip Galaxy tool if file is not bgzip-compressed."/>
53 <conditional name="filetype_cond">
54 <param name="filetype" type="select" label="Input filetype" help="-p. Set filetype of input file in case it is not detected properly.">
55 <option value="none" selected="True">None selected</option>
56 <option value="gff">GFF</option>
57 <option value="bed">BED</option>
58 <option value="sam">SAM</option>
59 <option value="vcf">VCF</option>
60 <option value="other">Other</option>
61 </param>
62 <when value="other">
63 <param name="seq_name_column" type="integer" optional="true" label="Sequence name column" help="-s" />
64 <param name="start_column" type="integer" optional="true" label="Start column" help="-b" />
65 <param name="end_column" type="integer" optional="true" label="End column" help="-e" />
66 <param name="skip_first_lines" type="integer" optional="true" label="Skip first n lines" help="-S" />
67 <param name="comment_symbol" type="text" label="Symbol for comment/meta lines" help="-c">
68 <sanitizer invalid_char="">
69 <valid initial="string.letters,string.digits"><add value="~`!@#$%^&amp;*()-_=+[{]}\|;:'&quot;,&lt;.&gt;?/ " /> </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>