Mercurial > repos > galaxyp > dbbuilder
diff dbbuilder.xml @ 0:487f80fb99ae draft
Uploaded
author | galaxyp |
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date | Wed, 19 Dec 2012 00:05:32 -0500 |
parents | |
children | 6c624803c5f9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dbbuilder.xml Wed Dec 19 00:05:32 2012 -0500 @@ -0,0 +1,46 @@ +<tool id="dbbuilder" version="0.1.0" name="Protein Database Downloader"> + <description> + </description> + <requirements> + <requirement type="binary">wget</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error computing FDR" /> + </stdio> + <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) + #elif $source.from == "cRAP" + #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" + #end if + wget -nv '$url' -O '${output_database}' + </command> + <inputs> + <conditional name="source"> + <param name="from" type="select" label="Download from"> + <option value="uniprot">UniProtKB</option> + <option value="cRAP">cRAP (contaminants)</option> + </param> + <when value="uniprot"> + <param name="taxon" type="select" format="text" > + <label>Taxonomy</label> + <options from_file="uniprot_taxons.loc"> + <column name="name" index="0" /> + <column name="value" index="1" /> + </options> + </param> + <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="fasta" name="output_database" label="Protein Database" /> + </outputs> + <help> +**Output** + +A FASTA file containing the specified protein sequences. + + </help> +</tool> +