Mercurial > repos > peterjc > sff_filter_by_id

comparison tools/filters/sff_filter_by_id.xml @ 1:9cd3591f6afa default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 0.0.2 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:25:08 -0400
parents eb852527b26c
children
comparison
equal deleted inserted replaced
0:eb852527b26c 1:9cd3591f6afa
1 <tool id="sff_filter_by_id" name="Filter SFF by ID" version="0.0.1"> 1 <tool id="sff_filter_by_id" name="Filter SFF by ID" version="0.0.2" hidden="true">
2 <description>from a tabular file</description> 2 <description>from a tabular file</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 sff_filter_by_id.py $input_tabular $columns $input_sff 4 sff_filter_by_id.py $input_tabular $columns $input_sff
5 #if $output_choice_cond.output_choice=="both" 5 #if $output_choice_cond.output_choice=="both"
6 $output_pos $output_neg 6 $output_pos $output_neg
41 <requirements> 41 <requirements>
42 <requirement type="python-module">Bio</requirement> 42 <requirement type="python-module">Bio</requirement>
43 </requirements> 43 </requirements>
44 <help> 44 <help>
45 45
46 **Deprecated**
47
48 This tool is now obsolete, and should not be used in future. It has been
49 replaced by a more general version covering FASTA, FASTQ and SFF in one
50 single tool.
51
46 **What it does** 52 **What it does**
47 53
48 By default it divides a Standard Flowgram Format (SFF) file in two, those 54 By default it divides a Standard Flowgram Format (SFF) file in two, those
49 sequences with or without an ID present in the tabular file column(s) specified. 55 sequences with or without an ID present in the tabular file column(s) specified.
50 You can opt to have a single output file of just the matching records, or just 56 You can opt to have a single output file of just the matching records, or just
60 BLASTN against a database of cloning vectors or bacteria, giving you a tabular 66 BLASTN against a database of cloning vectors or bacteria, giving you a tabular
61 file containing read identifiers. You could use this tool to extract only the 67 file containing read identifiers. You could use this tool to extract only the
62 reads without BLAST matches (i.e. those which do not match your contaminant 68 reads without BLAST matches (i.e. those which do not match your contaminant
63 database). 69 database).
64 70
65 ** Citation ** 71 **Citation**
66 72
67 This tool uses Biopython to read and write SFF files. If you use this tool in 73 This tool uses Biopython to read and write SFF files. If you use this tool in
68 scientific work leading to a publication, please cite the Biopython application 74 scientific work leading to a publication, please cite the Biopython application
69 note: 75 note:
70 76