Mercurial > repos > peterjc > seq_rename
comparison tools/filters/seq_rename.xml @ 0:a4b9836f8f47
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:43:26 -0400 |
parents | |
children | 9c8c5079c8af |
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1 <tool id="seq_rename" name="Rename sequences" version="0.0.1"> | |
2 <description>with ID mapping from a tabular file</description> | |
3 <command interpreter="python"> | |
4 seq_rename.py $input_tabular $old_column $new_column $input_file $input_file.ext $output_file | |
5 </command> | |
6 <inputs> | |
7 <param name="input_file" type="data" format="fasta,qual,fastq,sff" label="Sequence file" help="FASTA, QUAL, FASTQ, or SFF format." /> | |
8 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> | |
9 <param name="old_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing current (old) sequence identifiers"/> | |
10 <param name="new_column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column contai | |
11 ning new sequence identifiers"/> | |
12 </inputs> | |
13 <outputs> | |
14 <data name="output_file" format="fasta" label="Renamed ${on_string}"> | |
15 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> | |
16 <change_format> | |
17 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> | |
18 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> | |
19 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
20 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
21 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
22 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
23 </change_format> | |
24 </data> | |
25 </outputs> | |
26 <tests> | |
27 </tests> | |
28 <requirements> | |
29 <requirement type="python-module">Bio</requirement> | |
30 </requirements> | |
31 <help> | |
32 | |
33 **What it does** | |
34 | |
35 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a | |
36 new sequence file (of the same format) where the sequence identifiers have been | |
37 renamed according two the specified columns a the tabular file. | |
38 | |
39 WARNING: If you have any duplicates in the intput sequence file, you will still | |
40 have duplicate sequences in the output. | |
41 | |
42 WARNING: If the tabular file has more than one new name for any old ID, the | |
43 last one is used. | |
44 | |
45 **Citation** | |
46 | |
47 This tool uses Biopython to read and write SFF files. If you use this tool in | |
48 scientific work leading to a publication, please cite the Biopython application | |
49 note (and Galaxy too of course): | |
50 | |
51 Cock et al 2009. Biopython: freely available Python tools for computational | |
52 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
53 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
54 | |
55 </help> | |
56 </tool> |