comparison SMART/galaxy/coordinatesToSequence.xml @ 36:44d5973c188c

Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 15:02:29 -0400
parents
children
comparison
equal deleted inserted replaced
35:d94018ca4ada 36:44d5973c188c
1 <tool id="coordinatesToSequence" name="coordinates to sequence">
2 <description>Coordinates to Sequences: Extract the sequences from a list of coordinates.</description>
3 <command interpreter="python">
4 ../Java/Python/coordinatesToSequence.py -i $formatType.inputFileName1
5 #if $formatType.FormatInputFileName1 == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName1 == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName1 == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName1 == 'gff3':
12 -f gff3
13 #elif $formatType.FormatInputFileName1 == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName1 == 'gtf':
16 -f gtf
17 #end if
18
19 -s $sequence
20 -o $outputFileFasta
21
22 </command>
23
24 <inputs>
25 <conditional name="formatType">
26 <param name="FormatInputFileName1" type="select" label="Input File Format">
27 <option value="bed">bed</option>
28 <option value="gff">gff</option>
29 <option value="gff2">gff2</option>
30 <option value="gff3">gff3</option>
31 <option value="sam">sam</option>
32 <option value="gtf">gtf</option>
33 </param>
34 <when value="bed">
35 <param name="inputFileName1" format="bed" type="data" label="Input File"/>
36 </when>
37 <when value="gff">
38 <param name="inputFileName1" format="gff" type="data" label="Input File"/>
39 </when>
40 <when value="gff2">
41 <param name="inputFileName1" format="gff2" type="data" label="Input File"/>
42 </when>
43 <when value="gff3">
44 <param name="inputFileName1" format="gff3" type="data" label="Input File"/>
45 </when>
46 <when value="sam">
47 <param name="inputFileName1" format="sam" type="data" label="Input File"/>
48 </when>
49 <when value="gtf">
50 <param name="inputFileName1" format="gtf" type="data" label="Input File"/>
51 </when>
52 </conditional>
53
54 <param name="sequence" type="data" label="Reference fasta File" format="fasta"/>
55
56 </inputs>
57
58 <outputs>
59 <data name="outputFileFasta" format="fasta" label="coordinates to sequences output"/>
60 </outputs>
61
62 <help>
63 You can use this tool, if you just want to convert your mapping data to genomic coordinates, without any filtering. It requires a genomic coordinates file together with its format, an output format (GFF3, BED, etc...), the genome, and prints you the corresponding file.
64 </help>
65 </tool>