annotate fastx_reverse_complement.xml @ 1:e7c65e398bdd draft default tip

Deleted selected files
author idot
date Wed, 10 Jul 2013 06:16:21 -0400
parents 78a7d28f2a15
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
1 <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
2 <description></description>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
3 <command>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
4 cat '$input' |
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
5 fastx_reverse_complement
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
6 #if $input.ext == "fastqsanger":
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
7 -Q 33
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
8 #elif $input.ext == "fastq":
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
9 -Q 64
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
10 #end if
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
11 -v -o '$output'
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
12 </command>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
13 <inputs>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
14 <param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
15 </inputs>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
16
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
17 <tests>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
18 <test>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
19 <!-- Reverse-complement a FASTA file -->
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
20 <param name="input" value="fastx_rev_comp1.fasta" />
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
21 <output name="output" file="fastx_reverse_complement1.out" />
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
22 </test>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
23 <test>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
24 <!-- Reverse-complement a FASTQ file -->
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
25 <param name="input" value="fastx_rev_comp2.fastq" />
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
26 <output name="output" file="fastx_reverse_complement2.out" />
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
27 </test>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
28 </tests>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
29
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
30 <outputs>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
31 <data format="input" name="output" metadata_source="input"
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
32 />
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
33 </outputs>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
34
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
35 <help>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
36 **What it does**
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
37
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
38 This tool reverse-complements each sequence in a library.
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
39 If the library is a FASTQ, the quality-scores are also reversed.
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
40
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
41 --------
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
42
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
43 **Example**
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
44
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
45 Input FASTQ file::
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
46
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
47 @CSHL_1_FC42AGWWWXX:8:1:3:740
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
48 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
49 +CSHL_1_FC42AGWWWXX:8:1:3:740
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
50 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
51
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
52
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
53 Output FASTQ file::
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
54
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
55 @CSHL_1_FC42AGWWWXX:8:1:3:740
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
56 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
57 +CSHL_1_FC42AGWWWXX:8:1:3:740
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
58 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
59
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
60 ------
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
61
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
62 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
63
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
64 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
65
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
66 </help>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
67 </tool>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
68 <!-- FASTX-reverse-complement is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->