Mercurial > repos > peterjc > seq_select_by_id
comparison tools/filters/seq_select_by_id.xml @ 0:838b9bebfa3c
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 17:43:38 -0400 |
parents | |
children | 50a8a6917a9c |
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1 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.1"> | |
2 <description>from a tabular file</description> | |
3 <command interpreter="python"> | |
4 seq_select_by_id.py $input_tabular $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 to select from" 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="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> | |
10 </inputs> | |
11 <outputs> | |
12 <data name="output_file" format="fasta" label="Selected sequences"> | |
13 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> | |
14 <change_format> | |
15 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> | |
16 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> | |
17 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> | |
18 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> | |
19 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> | |
20 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> | |
21 </change_format> | |
22 </data> | |
23 </outputs> | |
24 <tests> | |
25 </tests> | |
26 <requirements> | |
27 <requirement type="python-module">Bio</requirement> | |
28 </requirements> | |
29 <help> | |
30 | |
31 **What it does** | |
32 | |
33 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a | |
34 new sequence file (of the same format) containing only the records with identifiers | |
35 in the tabular file (in the order from the tabular file). | |
36 | |
37 WARNING: If you have any duplicates in the tabular file identifiers, you will get | |
38 duplicate sequences in the output. | |
39 | |
40 **Citation** | |
41 | |
42 This tool uses Biopython to read, write and index sequence files. If you use | |
43 this tool in scientific work leading to a publication, please cite the | |
44 Biopython application note (and Galaxy too of course): | |
45 | |
46 Cock et al 2009. Biopython: freely available Python tools for computational | |
47 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. | |
48 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. | |
49 | |
50 </help> | |
51 </tool> |