Mercurial > repos > galaxyp > dbbuilder
comparison dbbuilder.xml @ 2:6c624803c5f9 draft
Update.
author | galaxyp |
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date | Fri, 10 May 2013 17:09:36 -0400 |
parents | 487f80fb99ae |
children | a38cd98a6b41 |
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1:abbd37e8bd14 | 2:6c624803c5f9 |
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1 <tool id="dbbuilder" version="0.1.0" name="Protein Database Downloader"> | 1 <tool id="dbbuilder" version="0.2.0" name="Protein Database Downloader"> |
2 <description> | 2 <description> |
3 </description> | 3 </description> |
4 <requirements> | 4 <requirements> |
5 <requirement type="binary">wget</requirement> | 5 <requirement type="binary">wget</requirement> |
6 </requirements> | 6 </requirements> |
7 <stdio> | 7 <stdio> |
8 <exit_code range="1:" level="fatal" description="Error computing FDR" /> | 8 <exit_code range="1:" level="fatal" description="Error downloading database." /> |
9 <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." /> | |
9 </stdio> | 10 </stdio> |
11 <!-- TODO: escape quotes. --> | |
12 <!-- Add NCBI and maxquant contaminants. --> | |
13 <!-- http://maxquant.org/contaminants.zip --> | |
14 <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz--> | |
10 <command> | 15 <command> |
11 #if $source.from == "uniprot" | 16 #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) | 17 #set $url = "http://www.uniprot.org/uniprot/?query=taxonomy%3a%22" + str($source.taxon) + "%22" + str($source.set) + str($source.reviewed) + "&force=yes&format=fasta" + str($source.include_isoform) |
18 #set $type = "direct" | |
13 #elif $source.from == "cRAP" | 19 #elif $source.from == "cRAP" |
14 #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" | 20 #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" |
21 #set $type = "direct" | |
22 #elif $source.from == "url" | |
23 #set $url = $source.url | |
24 #set $type = "direct" | |
15 #end if | 25 #end if |
26 #if $type =="direct" | |
16 wget -nv '$url' -O '${output_database}' | 27 wget -nv '$url' -O '${output_database}' |
28 #end if | |
17 </command> | 29 </command> |
18 <inputs> | 30 <inputs> |
19 <conditional name="source"> | 31 <conditional name="source"> |
20 <param name="from" type="select" label="Download from"> | 32 <param name="from" type="select" label="Download from"> |
21 <option value="uniprot">UniProtKB</option> | 33 <option value="uniprot">UniProtKB</option> |
22 <option value="cRAP">cRAP (contaminants)</option> | 34 <option value="cRAP">cRAP (contaminants)</option> |
35 <option value="url">Custom URL</option> | |
23 </param> | 36 </param> |
24 <when value="uniprot"> | 37 <when value="uniprot"> |
25 <param name="taxon" type="select" format="text" > | 38 <param name="taxon" type="select" format="text" > |
26 <label>Taxonomy</label> | 39 <label>Taxonomy</label> |
27 <options from_file="uniprot_taxons.loc"> | 40 <options from_file="uniprot_taxons.loc"> |
28 <column name="name" index="0" /> | 41 <column name="name" index="0" /> |
29 <column name="value" index="1" /> | 42 <column name="value" index="1" /> |
30 </options> | 43 </options> |
31 </param> | 44 </param> |
45 <param name="reviewed" type="select"> | |
46 <option value="+">UniProtKB</option> | |
47 <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option> | |
48 <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option> | |
49 <sanitizer> | |
50 <valid> | |
51 <add value="%"/> | |
52 </valid> | |
53 </sanitizer> | |
54 </param> | |
55 <param name="set" type="select" label="Proteome Set"> | |
56 <option value="+">Any</option> | |
57 <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option> | |
58 <option value="+keyword%3a181">Complete Proteome Set</option> | |
59 <sanitizer> | |
60 <valid> | |
61 <add value="%"/> | |
62 </valid> | |
63 </sanitizer> | |
64 </param> | |
32 <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" /> | 65 <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" /> |
66 </when> | |
67 <when value="cRAP" /> | |
68 <when value="url"> | |
69 <param name="url" value="" type="text" label="URL (http, ftp)"> | |
70 <sanitizer> | |
71 <valid> | |
72 <add value="%"/> | |
73 </valid> | |
74 </sanitizer> | |
75 </param> | |
33 </when> | 76 </when> |
34 </conditional> | 77 </conditional> |
35 </inputs> | 78 </inputs> |
36 <outputs> | 79 <outputs> |
37 <data format="fasta" name="output_database" label="Protein Database" /> | 80 <data format="fasta" name="output_database" label="Protein Database" /> |