Mercurial > repos > cpt > cpt_lipop_conversion
comparison cpt_lipop_conv/lipoP_to_gff3.xml @ 0:adde21b6bdb3 draft
Uploaded
author | cpt |
---|---|
date | Fri, 13 May 2022 05:18:31 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:adde21b6bdb3 |
---|---|
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> |