Mercurial > repos > galaxyp > dbbuilder
changeset 2:6c624803c5f9 draft
Update.
author | galaxyp |
---|---|
date | Fri, 10 May 2013 17:09:36 -0400 |
parents | abbd37e8bd14 |
children | a38cd98a6b41 |
files | dbbuilder.xml uniprot_taxons.loc.sample |
diffstat | 2 files changed, 49 insertions(+), 3 deletions(-) [+] |
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--- a/dbbuilder.xml Wed Dec 19 00:07:18 2012 -0500 +++ b/dbbuilder.xml Fri May 10 17:09:36 2013 -0400 @@ -1,25 +1,38 @@ -<tool id="dbbuilder" version="0.1.0" name="Protein Database Downloader"> +<tool id="dbbuilder" version="0.2.0" name="Protein Database Downloader"> <description> </description> <requirements> <requirement type="binary">wget</requirement> </requirements> <stdio> - <exit_code range="1:" level="fatal" description="Error computing FDR" /> + <exit_code range="1:" level="fatal" description="Error downloading database." /> + <regex match="ERROR" level="fatal" source="stderr" description="Error downloading database." /> </stdio> + <!-- TODO: escape quotes. --> + <!-- Add NCBI and maxquant contaminants. --> + <!-- http://maxquant.org/contaminants.zip --> + <!-- ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz--> <command> #if $source.from == "uniprot" - #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) + #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) + #set $type = "direct" #elif $source.from == "cRAP" #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" + #set $type = "direct" + #elif $source.from == "url" + #set $url = $source.url + #set $type = "direct" #end if + #if $type =="direct" wget -nv '$url' -O '${output_database}' + #end if </command> <inputs> <conditional name="source"> <param name="from" type="select" label="Download from"> <option value="uniprot">UniProtKB</option> <option value="cRAP">cRAP (contaminants)</option> + <option value="url">Custom URL</option> </param> <when value="uniprot"> <param name="taxon" type="select" format="text" > @@ -29,8 +42,38 @@ <column name="value" index="1" /> </options> </param> + <param name="reviewed" type="select"> + <option value="+">UniProtKB</option> + <option value="+reviewed%3Ayes">UniProtKB/Swiss-Prot (reviewed only)</option> + <option value="+reviewed%3Ano">UniProtKB/TrEMBL (unreviewed only)</option> + <sanitizer> + <valid> + <add value="%"/> + </valid> + </sanitizer> + </param> + <param name="set" type="select" label="Proteome Set"> + <option value="+">Any</option> + <option value="+keyword%3a1185" selected="true">Reference Proteome Set</option> + <option value="+keyword%3a181">Complete Proteome Set</option> + <sanitizer> + <valid> + <add value="%"/> + </valid> + </sanitizer> + </param> <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" /> </when> + <when value="cRAP" /> + <when value="url"> + <param name="url" value="" type="text" label="URL (http, ftp)"> + <sanitizer> + <valid> + <add value="%"/> + </valid> + </sanitizer> + </param> + </when> </conditional> </inputs> <outputs>
--- a/uniprot_taxons.loc.sample Wed Dec 19 00:07:18 2012 -0500 +++ b/uniprot_taxons.loc.sample Fri May 10 17:09:36 2013 -0400 @@ -5,3 +5,6 @@ Sus scrofa (Pig) 9823 Escherichia coli (strain K12) 83333 Arabidopsis thaliana (Mouse-ear cress) 3702 +Caenorhabditis elegans (C.elegans) 6239 +Drosophila melanogaster (Fruit fly) 7227 +Saccharomyces cerevisiae (Baker's Yeast) 4932 \ No newline at end of file