Mercurial > repos > devteam > fastx_reverse_complement
annotate fastx_reverse_complement.xml @ 1:a710c1b9776b
Remove spurious version strings.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Tue, 26 Nov 2013 12:49:47 -0500 |
| parents | 03d7d89fddaa |
| children | 43540312cb76 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="cshl_fastx_reverse_complement" version="1.0.0" name="Reverse-Complement"> |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
| 5 </requirements> | |
| 6 <command>zcat -f '$input' | fastx_reverse_complement -v -o $output | |
| 7 #if $input.ext == "fastqsanger": | |
| 8 -Q 33 | |
| 9 #end if | |
| 10 </command> | |
| 11 <inputs> | |
|
1
a710c1b9776b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
12 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" /> |
| 0 | 13 </inputs> |
| 14 | |
| 15 <tests> | |
| 16 <test> | |
| 17 <!-- Reverse-complement a FASTA file --> | |
|
1
a710c1b9776b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
18 <param name="input" value="fastx_rev_comp1.fasta" /> |
|
a710c1b9776b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
19 <output name="output" file="fastx_reverse_complement1.out" /> |
| 0 | 20 </test> |
| 21 <test> | |
| 22 <!-- Reverse-complement a FASTQ file --> | |
|
1
a710c1b9776b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
23 <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/> |
|
a710c1b9776b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
24 <output name="output" file="fastx_reverse_complement2.out" /> |
| 0 | 25 </test> |
| 26 </tests> | |
| 27 | |
| 28 | |
| 29 <outputs> | |
|
1
a710c1b9776b
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
30 <data format="input" name="output" metadata_source="input" /> |
| 0 | 31 </outputs> |
| 32 | |
| 33 <help> | |
| 34 **What it does** | |
| 35 | |
| 36 This tool reverse-complements each sequence in a library. | |
| 37 If the library is a FASTQ, the quality-scores are also reversed. | |
| 38 | |
| 39 -------- | |
| 40 | |
| 41 **Example** | |
| 42 | |
| 43 Input FASTQ file:: | |
| 44 | |
| 45 @CSHL_1_FC42AGWWWXX:8:1:3:740 | |
| 46 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA | |
| 47 +CSHL_1_FC42AGWWWXX:8:1:3:740 | |
| 48 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 | |
| 49 | |
| 50 | |
| 51 Output FASTQ file:: | |
| 52 | |
| 53 @CSHL_1_FC42AGWWWXX:8:1:3:740 | |
| 54 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA | |
| 55 +CSHL_1_FC42AGWWWXX:8:1:3:740 | |
| 56 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 | |
| 57 | |
| 58 ------ | |
| 59 | |
| 60 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
| 61 | |
| 62 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
| 63 | |
| 64 </help> | |
| 65 </tool> |