Mercurial > repos > devteam > fastx_artifacts_filter
annotate fastx_artifacts_filter.xml @ 1:c8808979ba33
Removed excess version attributes.
author | Dave Bouvier <dave@bx.psu.edu> |
---|---|
date | Tue, 03 Dec 2013 12:36:13 -0500 |
parents | 7f9660a246c0 |
children | 09070cacefd8 |
rev | line source |
---|---|
0 | 1 <tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts"> |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
5 </requirements> | |
6 <command>zcat -f '$input' | fastx_artifacts_filter -v -o "$output" | |
7 #if $input.ext == "fastqsanger": | |
8 -Q 33 | |
9 #end if | |
10 </command> | |
11 | |
12 <inputs> | |
1
c8808979ba33
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
13 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" /> |
0 | 14 |
15 </inputs> | |
16 | |
17 <tests> | |
18 <test> | |
19 <!-- Filter FASTA file --> | |
1
c8808979ba33
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
20 <param name="input" value="fastx_artifacts1.fasta" /> |
c8808979ba33
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
21 <param name="output" file="fastx_artifacts1.out" /> |
0 | 22 </test> |
23 <test> | |
24 <!-- Filter FASTQ file --> | |
1
c8808979ba33
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
25 <param name="input" value="fastx_artifacts2.fastq" ftype="fastqsanger" /> |
c8808979ba33
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
26 <param name="output" file="fastx_artifacts2.out" /> |
0 | 27 </test> |
28 </tests> | |
29 | |
30 <outputs> | |
1
c8808979ba33
Removed excess version attributes.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
31 <data format="input" name="output" metadata_source="input" /> |
0 | 32 </outputs> |
33 <help> | |
34 **What it does** | |
35 | |
36 This tool filters sequencing artifacts (reads with all but 3 identical bases). | |
37 | |
38 -------- | |
39 | |
40 **The following is an example of sequences which will be filtered out**:: | |
41 | |
42 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
43 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
44 AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
45 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
46 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
47 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
48 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAA | |
49 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
50 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
51 AAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
52 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
53 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
54 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC | |
55 AAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
56 AAAAAAAAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
57 AAAAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA | |
58 AAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
59 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAA | |
60 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
61 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAA | |
62 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA | |
63 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAA | |
64 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAA | |
65 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAA | |
66 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAA | |
67 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAA | |
68 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAA | |
69 AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
70 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAA | |
71 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
72 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAA | |
73 AAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
74 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAA | |
75 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
76 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAA | |
77 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAA | |
78 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA | |
79 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
80 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA | |
81 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAAAAA | |
82 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAA | |
83 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAA | |
84 | |
85 ------ | |
86 | |
87 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
88 | |
89 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
90 </help> | |
91 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> | |
92 </tool> |