Mercurial > repos > cpt_testbed > suite_work2
comparison fasta_remove_id.xml @ 0:d5c3354c166d draft default tip
Uploaded
author | cpt_testbed |
---|---|
date | Fri, 29 Apr 2022 10:33:36 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:d5c3354c166d |
---|---|
1 <?xml version="1.0"?> | |
2 <tool id="edu.tamu.cpt.fasta.remove_desc" name="Remove Description" version="19.1.0.0"> | |
3 <description>from fasta file</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 <import>cpt-macros.xml</import> | |
7 </macros> | |
8 <expand macro="requirements"/> | |
9 <command detect_errors="aggressive"> | |
10 $__tool_directory__/fasta_remove_id.py | |
11 @SEQUENCE@ | |
12 > $out | |
13 </command> | |
14 <inputs> | |
15 <expand macro="input/fasta" /> | |
16 </inputs> | |
17 <outputs> | |
18 <data format="fasta" name="out" /> | |
19 </outputs> | |
20 <tests> | |
21 <test> | |
22 <param name="sequences" value="T7_RemIDIn.fasta"/> | |
23 <output name="out" file="T7_RemIDOut.fasta" /> | |
24 </test> | |
25 </tests> | |
26 <help> | |
27 **What it does** | |
28 | |
29 From an input FASTA file, removes the "description" field (all characters after | |
30 the first space in the top line until a return) after the FASTA ID (from the > | |
31 to the first space). | |
32 | |
33 This is a permanent removal of the description. It is useful for tools that | |
34 behave in unexpected ways if it is present, e.g. Glimmer/GeneMarkS. | |
35 | |
36 **Example Input/Output** | |
37 | |
38 For an input FASTA file:: | |
39 | |
40 >1|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 288 bp | |
41 acttacgcggagagatgagaccaacgctcgcctaggggcacgcttgtaattgacttatct | |
42 >2|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 232 bp | |
43 gttggggacccacctatcagggagtgtagtagtataagactgtccaataccccccaacat | |
44 | |
45 The resulting FASTA will contain only IDs without a description:: | |
46 | |
47 >1|random | |
48 acttacgcggagagatgagaccaacgctcgcctaggggcacgcttgtaattgacttatct | |
49 >2|random | |
50 gttggggacccacctatcagggagtgtagtagtataagactgtccaataccccccaacat | |
51 </help> | |
52 <expand macro="citations" /> | |
53 </tool> |