0
|
1 <tool id="edu.tamu.cpt.gff3.lipoP_to_gff3" name= "LipoP to GFF3" version="1.0">
|
|
2 <description>Adds LipoP results to GFF3</description>
|
|
3 <macros>
|
|
4 <import>macros.xml</import>
|
|
5 <import>cpt-macros.xml</import>
|
|
6 </macros>
|
|
7 <expand macro="requirements"/>
|
|
8 <command detect_errors="aggressive"><![CDATA[
|
|
9 python $__tool_directory__/lipoP_to_gff3.py
|
|
10
|
|
11 "$lipoIn"
|
|
12 "$gff3In"
|
|
13 --jBrowseOut "$jBrowseOut"
|
|
14 $filterSP2
|
|
15 > $stdout
|
|
16
|
|
17 ]]></command>
|
|
18 <inputs>
|
|
19 <param label="LipoP Output" name="lipoIn" type="data" format="txt"/>
|
|
20 <param label="GFF3 for Rebasing" name="gff3In" type="data" format="gff3"/>
|
|
21 <param label="Output to jBrowse" name="jBrowseOut" type="boolean" truevalue="True" falsevalue="" help="Strip non-cleavage features from GFF3 (for viewing in Apollo)"/>
|
|
22 <param name="filterSP2" truevalue="--filterSP2" falsevalue="" type="boolean" label="Filter for only SPII Cleavage sites" checked="true"/>
|
|
23 </inputs>
|
|
24 <outputs>
|
|
25 <data format="gff3" name="stdout"/>
|
|
26 </outputs>
|
|
27 <tests>
|
|
28 <test>
|
|
29 <param name="lipoIn" value="LipoToGFF_In.txt" />
|
|
30 <param name="gff3In" value="LipoToGFF_In.gff3" />
|
|
31 <param name="jBrowseOut" value="True" />
|
|
32 <param name="filterSP2" value="True" />
|
|
33 <output name="stdout" value="LipoToGFF_Out.gff3" />
|
|
34 </test>
|
|
35 </tests>
|
|
36 <help><![CDATA[
|
|
37 **What it does**
|
|
38
|
|
39 Adds the cleavage sites from a LipoP run to a GFF3 file's feature list. Must use
|
|
40 the .txt output of LipoP (ensure .html is turned off). The most common way this
|
|
41 tool will be utilized is to take a GFF3, use the GFF3 Feature Sequence Export
|
|
42 tool (https://cpt.tamu.edu/galaxy/root?tool_id=edu.tamu.cpt.gff3.export_seq) to
|
|
43 get a multi-FASTA of the CDSs, run that multi-FASTA through LipoP, and then
|
|
44 recombine the LipoP results with the original GFF3 file with this tool.
|
|
45
|
|
46 Currently, only CleavII results will be added with this tool.
|
|
47
|
|
48 "Output to jBrowse" will remove all gene features that do not have a CleavII
|
|
49 result from the LipoP, and remove all sub features of the gene except for the
|
|
50 cleavage sites. This is useful for viewing in Apollo, but should most likely
|
|
51 not be used if you plan to run this output through more tools.
|
|
52 ]]></help>
|
|
53 <expand macro="citations-2020" />
|
|
54 </tool>
|