comparison fasta_remove_id.xml @ 0:d5c3354c166d draft default tip

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author cpt_testbed
date Fri, 29 Apr 2022 10:33:36 +0000
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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_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>