Mercurial > repos > galaxyp > dbbuilder
comparison dbbuilder.xml @ 0:487f80fb99ae draft
Uploaded
author | galaxyp |
---|---|
date | Wed, 19 Dec 2012 00:05:32 -0500 |
parents | |
children | 6c624803c5f9 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:487f80fb99ae |
---|---|
1 <tool id="dbbuilder" version="0.1.0" name="Protein Database Downloader"> | |
2 <description> | |
3 </description> | |
4 <requirements> | |
5 <requirement type="binary">wget</requirement> | |
6 </requirements> | |
7 <stdio> | |
8 <exit_code range="1:" level="fatal" description="Error computing FDR" /> | |
9 </stdio> | |
10 <command> | |
11 #if $source.from == "uniprot" | |
12 #set $url = "http://www.uniprot.org/uniprot/?query=taxonomy%3a%22" + str($source.taxon) + "%22+keyword%3a1185&force=yes&format=fasta" + str($source.include_isoform) | |
13 #elif $source.from == "cRAP" | |
14 #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" | |
15 #end if | |
16 wget -nv '$url' -O '${output_database}' | |
17 </command> | |
18 <inputs> | |
19 <conditional name="source"> | |
20 <param name="from" type="select" label="Download from"> | |
21 <option value="uniprot">UniProtKB</option> | |
22 <option value="cRAP">cRAP (contaminants)</option> | |
23 </param> | |
24 <when value="uniprot"> | |
25 <param name="taxon" type="select" format="text" > | |
26 <label>Taxonomy</label> | |
27 <options from_file="uniprot_taxons.loc"> | |
28 <column name="name" index="0" /> | |
29 <column name="value" index="1" /> | |
30 </options> | |
31 </param> | |
32 <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" /> | |
33 </when> | |
34 </conditional> | |
35 </inputs> | |
36 <outputs> | |
37 <data format="fasta" name="output_database" label="Protein Database" /> | |
38 </outputs> | |
39 <help> | |
40 **Output** | |
41 | |
42 A FASTA file containing the specified protein sequences. | |
43 | |
44 </help> | |
45 </tool> | |
46 |