Mercurial > repos > curtisross > remove_fasta_description
comparison fasta_remove_id.xml @ 1:d85af06ab3db draft
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author | curtisross |
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date | Thu, 23 Sep 2021 16:25:45 +0000 |
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0:2b42545705fa | 1:d85af06ab3db |
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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_DESC.fasta"/> | |
23 <output name="out" file="T7_CLEAN.fasta" /> | |
24 </test> | |
25 <test> | |
26 <param name="sequences" value="regex.a3.fa"/> | |
27 <output name="out" file="regex.a3.clean.fa" /> | |
28 </test> | |
29 </tests> | |
30 <help> | |
31 **What it does** | |
32 | |
33 From an input FASTA file, removes the "description" field (all characters after | |
34 the first space in the top line until a return) after the FASTA ID (from the > | |
35 to the first space). | |
36 | |
37 This is a permanent removal of the description. It is useful for tools that | |
38 behave in unexpected ways if it is present, e.g. Glimmer/GeneMarkS. | |
39 | |
40 **Example Input/Output** | |
41 | |
42 For an input FASTA file:: | |
43 | |
44 >1|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 288 bp | |
45 acttacgcggagagatgagaccaacgctcgcctaggggcacgcttgtaattgacttatct | |
46 >2|random sequence|A: 0.25|C: 0.25|G: 0.25|T: 0.25|length: 232 bp | |
47 gttggggacccacctatcagggagtgtagtagtataagactgtccaataccccccaacat | |
48 | |
49 The resulting FASTA will contain only IDs without a description:: | |
50 | |
51 >1|random | |
52 acttacgcggagagatgagaccaacgctcgcctaggggcacgcttgtaattgacttatct | |
53 >2|random | |
54 gttggggacccacctatcagggagtgtagtagtataagactgtccaataccccccaacat | |
55 </help> | |
56 <expand macro="citations" /> | |
57 </tool> |