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comparison fimo_gff_to_gff.xml @ 0:48d424adfaef draft

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author greg
date Thu, 03 Mar 2016 21:16:32 -0500
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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&lt;designation&gt;.*)" 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44 @unpublished{None,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>