Mercurial > repos > peterjc > seq_primer_clip
comparison tools/seq_primer_clip/seq_primer_clip.xml @ 2:ee5acea162a7 draft
Uploaded v0.0.10, README now using RST, MIT licence, automatic Biopython dependency
author | peterjc |
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date | Thu, 24 Oct 2013 09:37:25 -0400 |
parents | |
children | 9b074c1db68e |
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1:8c02a91a8680 | 2:ee5acea162a7 |
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1 <tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.10"> | |
2 <description>Trim off 5' or 3' primers</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.62">biopython</requirement> | |
5 <requirement type="python-module">Bio</requirement> | |
6 </requirements> | |
7 <version_command interpreter="python">seq_primer_clip.py --version</version_command> | |
8 <command interpreter="python"> | |
9 seq_primer_clip.py $input_file $input_file.ext $primer_fasta $primer_type $mm $min_len $keep_negatives $output_file | |
10 </command> | |
11 <stdio> | |
12 <!-- Anything other than zero is an error --> | |
13 <exit_code range="1:" /> | |
14 <exit_code range=":-1" /> | |
15 </stdio> | |
16 <inputs> | |
17 <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to clip" description="FASTA, FASTQ, or SFF format."/> | |
18 <param name="primer_fasta" type="data" format="fasta" label="FASTA file containing primer(s)"/> | |
19 <param name="primer_type" type="select" label="Type of primers"> | |
20 <option value="Forward">Forward (5') primers</option> | |
21 <option value="Reverse">Reverse (3') primers (given with respect to the forward strand)</option> | |
22 <option value="Reverse-complement">Reverse (3') primers (given with respect to the reverse strand)</option> | |
23 </param> | |
24 <param name="mm" type="integer" value="0" label="How many mismatches to allow? (0, 1 or 2)"> | |
25 <validator type="in_range" min="0" max="2" /> | |
26 </param> | |
27 <param name="keep_negatives" type="boolean" value="false" label="Keep reads with no matched primer"/> | |
28 <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/> | |
29 </inputs> | |
30 <outputs> | |
31 <data name="output_file" format="data" label="$primer_type primer clipped"> | |
32 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> | |
33 <change_format> | |
34 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> | |
35 <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" /> | |
36 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> | |
37 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
38 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
39 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
40 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
41 </change_format> | |
42 </data> | |
43 </outputs> | |
44 <tests> | |
45 <test> | |
46 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fasta" ftype="fasta" /> | |
47 <param name="primer_fasta" value="dop_primers.fasta" /> | |
48 <param name="primer_type" value="Forward" /> | |
49 <param name="mm" value="2" /> | |
50 <param name="keep_negatives" value="false" /> | |
51 <param name="min_len" value="35" /> | |
52 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> | |
53 </test> | |
54 <test> | |
55 <param name="input_file" value="MID4_GLZRM4E04_rnd30.fastqsanger" ftype="fastqsanger" /> | |
56 <param name="primer_fasta" value="dop_primers.fasta" /> | |
57 <param name="primer_type" value="Forward" /> | |
58 <param name="mm" value="2" /> | |
59 <param name="keep_negatives" value="false" /> | |
60 <param name="min_len" value="35" /> | |
61 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> | |
62 </test> | |
63 <test> | |
64 <param name="input_file" value="MID4_GLZRM4E04_rnd30.sff" ftype="sff" /> | |
65 <param name="primer_fasta" value="dop_primers.fasta" /> | |
66 <param name="primer_type" value="Forward" /> | |
67 <param name="mm" value="2" /> | |
68 <param name="keep_negatives" value="false" /> | |
69 <param name="min_len" value="35" /> | |
70 <output name="output_file" file="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> | |
71 </test> | |
72 <test> | |
73 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fasta" ftype="fasta" /> | |
74 <param name="primer_fasta" value="dop_primers.fasta" /> | |
75 <param name="primer_type" value="Reverse" /> | |
76 <param name="mm" value="2" /> | |
77 <param name="keep_negatives" value="true" /> | |
78 <param name="min_len" value="35" /> | |
79 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fasta" ftype="fasta" /> | |
80 </test> | |
81 <test> | |
82 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.fastqsanger" ftype="fastqsanger" /> | |
83 <param name="primer_fasta" value="dop_primers.fasta" /> | |
84 <param name="primer_type" value="Reverse" /> | |
85 <param name="mm" value="2" /> | |
86 <param name="keep_negatives" value="true" /> | |
87 <param name="min_len" value="35" /> | |
88 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.fastqsanger" ftype="fastqsanger" /> | |
89 </test> | |
90 <test> | |
91 <param name="input_file" value="MID4_GLZRM4E04_rnd30_fclip.sff" ftype="sff" /> | |
92 <param name="primer_fasta" value="dop_primers.fasta" /> | |
93 <param name="primer_type" value="Reverse" /> | |
94 <param name="mm" value="2" /> | |
95 <param name="keep_negatives" value="true" /> | |
96 <param name="min_len" value="35" /> | |
97 <output name="output_file" file="MID4_GLZRM4E04_rnd30_frclip.sff" ftype="sff" /> | |
98 </test> | |
99 </tests> | |
100 <requirements> | |
101 <requirement type="python-module">Bio</requirement> | |
102 </requirements> | |
103 <help> | |
104 | |
105 **What it does** | |
106 | |
107 Looks for the given primer sequences (within the existing clipped sequence) and | |
108 further clips the reads to remove the primers and any preceding/trailing sequence. | |
109 | |
110 Reads containing a forward primer are reduced to just the sequence after (and | |
111 excluding) the forward primer. | |
112 | |
113 Reads containing a reverse primer are reduced to just the sequence before (and | |
114 excluding) the reverse primer. | |
115 | |
116 Degenerate primers can be specified using the standard IUPAC ambiguity codes, | |
117 thus a primer with an N would match A, C, T or G (or any of the IUPAC ambiguity | |
118 codes) and so on. | |
119 | |
120 Note that for SFF files only the clip/trim positions are edited - you will still | |
121 be able to extract the original full read (with any adapter sequence and poor | |
122 quality sequence) if you need to. | |
123 | |
124 .. class:: warningmark | |
125 | |
126 **Note**. This tool was initially written for Roche 454 data, and should also | |
127 work fine on Sanger or Ion Torrent as well. However, it is probably too slow | |
128 for use on large Illumina datasets. | |
129 | |
130 | |
131 **Citation** | |
132 | |
133 This tool uses Biopython. If you use this tool in scientific work leading to a | |
134 publication, please cite: | |
135 | |
136 Cock et al 2009. Biopython: freely available Python tools for computational | |
137 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
138 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
139 | |
140 This tool is available to install into other Galaxy Instances via the Galaxy | |
141 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip | |
142 </help> | |
143 </tool> |