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comparison fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit_with_gzip_and_output_label/fastx_trimmer.xml @ 3:997f5136985f draft default tip
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author | xilinxu |
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date | Thu, 14 Aug 2014 04:52:17 -0400 |
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2:dfe9332138cf | 3:997f5136985f |
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1 <tool id="cshl_fastx_trimmer" name="Trim"> | |
2 <description>sequences</description> | |
3 <command>zcat -f '$input' | fastx_trimmer $GZIPOUT -v -f $first -l $last -o $output</command> | |
4 | |
5 <inputs> | |
6 <param format="fasta,fastqsolexa" name="input" type="data" label="Library to clip" /> | |
7 | |
8 <param name="first" size="4" type="integer" value="1"> | |
9 <label>First base to keep</label> | |
10 </param> | |
11 | |
12 <param name="last" size="4" type="integer" value="21"> | |
13 <label>Last base to keep</label> | |
14 </param> | |
15 | |
16 <param name="GZIPOUT" type="select" label="Compress output file (using GZIP) "> | |
17 <option value="-z">yes</option> | |
18 <option value="">no</option> | |
19 </param> | |
20 </inputs> | |
21 | |
22 <tests> | |
23 <test> | |
24 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) --> | |
25 <param name="input" value="fastx_trimmer1.fasta" /> | |
26 <param name="first" value="5"/> | |
27 <param name="last" value="36"/> | |
28 <param name="GZIPOUT" value=""/> | |
29 <output name="output" file="fastx_trimmer1.out" /> | |
30 </test> | |
31 <test> | |
32 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) --> | |
33 <param name="input" value="fastx_trimmer2.fastq" /> | |
34 <param name="first" value="1"/> | |
35 <param name="last" value="27"/> | |
36 <param name="GZIPOUT" value=""/> | |
37 <output name="output" file="fastx_trimmer2.out" /> | |
38 </test> | |
39 </tests> | |
40 | |
41 <outputs> | |
42 <data format="input" name="output" label="$input.tag trimmed" metadata_source="input" /> | |
43 </outputs> | |
44 <help> | |
45 **What it does** | |
46 | |
47 This tool trims (cut bases from) sequences in a FASTA/Q file. | |
48 | |
49 -------- | |
50 | |
51 **Example** | |
52 | |
53 Input Fasta file (with 36 bases in each sequences):: | |
54 | |
55 >1-1 | |
56 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC | |
57 >2-1 | |
58 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA | |
59 | |
60 | |
61 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base):: | |
62 | |
63 >1-1 | |
64 TATGGTCAGAAACCATATGCA | |
65 >2-1 | |
66 CAGCGAGGCTTTAATGCCATT | |
67 | |
68 Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences:: | |
69 | |
70 >1-1 | |
71 TCAGA | |
72 >2-1 | |
73 AGGCT | |
74 | |
75 </help> | |
76 </tool> | |
77 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |