Mercurial > repos > galaxyp > dbbuilder
view dbbuilder.xml @ 5:1d3557cec567 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
author | galaxyp |
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date | Sat, 29 Apr 2017 09:46:31 -0400 |
parents | |
children | 19ee2e85931a |
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<tool id="dbbuilder" name="Protein Database Downloader" version="0.2.1"> <description></description> <requirements> <requirement type="package">gnu-wget</requirement> </requirements> <stdio> <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> <![CDATA[ #if $source.from == "uniprot" #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 $url = "https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.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" help="Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a corss species collection of functional protein databases"> <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" help="select species for protein database"> <label>Taxonomy</label> <options from_file="uniprot_taxons.loc"> <column name="name" index="0" /> <column name="value" index="1" /> </options> </param> <param name="reviewed" type="select" help="UniProtKB/TrEMBL (unreviewed)is a large, automatically annotated database- may contain redundant sequences, but there is a higher chance peptides will be identified. UniProtKB/Swiss-Prot (reviewed) is a smaller, manually annotated database- less of a chance peptides will be identified but less sequence redundancy"> <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" help="several different forms of a given protein are incorporated into database" /> </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> <data format="fasta" name="output_database" label="Protein Database" /> </outputs> <tests> <test> <param name="from" value="cRAP" /> <output name="output_database"> <assert_contents> <has_text text="KKA1_ECOLX" /> </assert_contents> </output> </test> </tests> <help> <![CDATA[ **Output** Creates a FASTA file of specified protein sequences for comparison with experimental MS/MS data in search algorithm. **External Links** _Galaxy-P 101 shows usage Protein Database Downloader tool in the creation of a workflow .. _Galaxy-P 101: http://msi-galaxy-p.readthedocs.org/en/latest/sections/galaxyp_101.html _UniProtKB provides additional information about the UniProt Knowledgebase .. _UniProtKB: http://www.uniprot.org/help/uniprotkb ]]> </help> </tool>