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comparison fastx_trimmer_from_end.xml @ 0:78a7d28f2a15 draft

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author idot
date Wed, 10 Jul 2013 06:13:48 -0400
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1 <tool id="cshl_fastx_end_trimmer" name="Trim End">
2 <description>of sequences</description>
3 <command>
4 cat '$input' |
5 fastx_trimmer
6 #if $input.ext == "fastqsanger":
7 -Q 33
8 #elif $input.ext == "fastq":
9 -Q 64
10 #end if
11 -v -t $trimnum -m $minlen -o '$output'
12 </command>
13 <inputs>
14 <param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to clip" />
15
16 <param name="trimnum" size="4" type="integer" value="5">
17 <label>Number of nucleotides to be trimmed</label>
18 <help>This will trim from the end of the sequences</help>
19 </param>
20
21 <param name="minlen" size="4" type="integer" value="10">
22 <label>Minimum sequence length</label>
23 <help>Sequences shorter than this length will be discarded</help>
24 </param>
25 </inputs>
26
27 <tests>
28 <test>
29 <param name="input" value="fastx_trimmer_from_end1.fasta" />
30 <param name="trimnum" value="2"/>
31 <param name="minlen" value="16"/>
32 <output name="output" file="fastx_trimmer_from_end1.out" />
33 </test>
34 </tests>
35
36 <outputs>
37 <data format="input" name="output" metadata_source="input"
38 />
39 </outputs>
40 <help>
41 **What it does**
42
43 This tool trims (cut nucleotides from) sequences in a FASTQ/FASTA file from the 3' end.
44
45 .. class:: infomark
46
47 When trimming a FASTQ file, the quality scores will be trimmed appropriately (to the same length of the corresponding sequence).
48
49 --------
50
51 **Example**
52
53 Input Fasta file::
54
55 >1-1
56 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
57 >2-1
58 CAGCGAGGCTTTAATGCCATT
59
60
61 Trimming 5 nucleotides from the end, and discarding sequences shorter than 10 , we get the following FASTA file::
62
63 >1-1
64 TATGGTCAGAAACCATATGCAGAGCCTGTAG
65 >2-1
66 CAGCGAGGCTTTAATG
67
68 Trimming 10 nucleotides from the end, and discarding sequences shorter than 15 , we get the following FASTA file::
69
70 >1-1
71 TATGGTCAGAAACCATATGCAGAGCC
72
73 ------
74
75 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
76
77 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
78
79 </help>
80 </tool>
81 <!-- FASTX-Trimmer-End is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->