Mercurial > repos > peterjc > seq_select_by_id
annotate 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 |
---|---|
date | Tue, 07 Jun 2011 17:43:38 -0400 |
parents | |
children | 50a8a6917a9c |
rev | line source |
---|---|
0
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
1 <tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.1"> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
2 <description>from a tabular file</description> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
3 <command interpreter="python"> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
4 seq_select_by_id.py $input_tabular $column $input_file $input_file.ext $output_file |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
5 </command> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
6 <inputs> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
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." /> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
8 <param name="input_tabular" type="data" format="tabular" label="Tabular file containing sequence identifiers"/> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
9 <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
10 </inputs> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
11 <outputs> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
12 <data name="output_file" format="fasta" label="Selected sequences"> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
13 <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
14 <change_format> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
15 <when input_dataset="input_file" attribute="extension" value="sff" format="sff" /> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
16 <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" /> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
17 <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" /> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
18 <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
19 <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" /> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
20 <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
21 </change_format> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
22 </data> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
23 </outputs> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
24 <tests> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
25 </tests> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
26 <requirements> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
27 <requirement type="python-module">Bio</requirement> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
28 </requirements> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
29 <help> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
30 |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
31 **What it does** |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
32 |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
33 Takes a FASTA, QUAL, FASTQ or Standard Flowgram Format (SFF) file and produces a |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
34 new sequence file (of the same format) containing only the records with identifiers |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
35 in the tabular file (in the order from the tabular file). |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
36 |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
37 WARNING: If you have any duplicates in the tabular file identifiers, you will get |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
38 duplicate sequences in the output. |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
39 |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
40 **Citation** |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
41 |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
42 This tool uses Biopython to read, write and index sequence files. If you use |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
43 this tool in scientific work leading to a publication, please cite the |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
44 Biopython application note (and Galaxy too of course): |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
45 |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
46 Cock et al 2009. Biopython: freely available Python tools for computational |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
47 molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
48 http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878. |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
49 |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
50 </help> |
838b9bebfa3c
Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff
changeset
|
51 </tool> |