|
0
|
1 <tool id="fimo_gff_to_gff" name="Fimo Gff to Gff" version="1.0.0">
|
|
|
2 <description></description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="5.18.1">perl</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command>
|
|
|
7 <![CDATA[
|
|
|
8 mkdir -p output &&
|
|
|
9 perl $__tool_directory__/fimo_gff_to_gff.pl "$input" output
|
|
|
10 ]]>
|
|
|
11 </command>
|
|
|
12 <inputs>
|
|
|
13 <param name="input" type="data" format="tabular" label="FIMO (almost) Gff input" />
|
|
|
14 </inputs>
|
|
|
15 <outputs>
|
|
|
16 <collection name="motifs" type="list" label="Motifs: ${tool.name} on ${on_string}">
|
|
|
17 <discover_datasets pattern="(?P<designation>.*)" directory="output" ext="gff" visible="false" />
|
|
|
18 </collection>
|
|
|
19 </outputs>
|
|
|
20 <tests>
|
|
|
21 <test>
|
|
|
22 <param name="input" value="input.tabular" ftype="tabular" />
|
|
|
23 <output_collection name="motifs" type="list">
|
|
|
24 <element name="MOTIF1" file="motif1.gff" ftype="gff"/>
|
|
|
25 </output_collection>
|
|
|
26 </test>
|
|
|
27 </tests>
|
|
|
28 <help>
|
|
|
29
|
|
|
30 .. class:: warningmark
|
|
|
31
|
|
|
32 This tool requires FASTA headers that use the default bedtools getfasta header format of
|
|
|
33 **chrom:start-stop(strand)** or **chrom:start-stop** in which case strand is set as '+'
|
|
|
34 per the bedtools standard.
|
|
|
35
|
|
|
36 **What it does**
|
|
|
37
|
|
|
38 Converts FIMO tabular (almost GFF) files to true genomic coordinates in valid GFF format. A
|
|
|
39 collection of datasets is produced consisting of one dataset per motif discovered in the input.
|
|
|
40
|
|
|
41 </help>
|
|
|
42 <citations>
|
|
|
43 <citation type="bibtex">
|
|
|
44 @unpublished{None,
|
|
|
45 author = {Lai, William},
|
|
|
46 title = {None},
|
|
|
47 year = {None},
|
|
|
48 eprint = {None},
|
|
|
49 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
|
|
|
50 }</citation>
|
|
|
51 </citations>
|
|
|
52 </tool>
|
