Mercurial > repos > galaxyp > dbbuilder
changeset 11:8e637098a8ab draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder commit 16ba4570b04301b774ee0420694f379cc640744b
| author | galaxyp |
|---|---|
| date | Tue, 27 Sep 2022 13:22:04 +0000 |
| parents | e9df53a75f3c |
| children | 983bf725dfc2 |
| files | dbbuilder.xml uniprotkb.py |
| diffstat | 2 files changed, 103 insertions(+), 12 deletions(-) [+] |
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--- a/dbbuilder.xml Wed Nov 25 17:43:51 2020 +0000 +++ b/dbbuilder.xml Tue Sep 27 13:22:04 2022 +0000 @@ -1,7 +1,9 @@ -<tool id="dbbuilder" name="Protein Database Downloader" version="0.3.2"> +<tool id="dbbuilder" name="Protein Database Downloader" version="0.3.3"> <description></description> <requirements> <requirement type="package" version="1.20.1">wget</requirement> + <requirement type="package" version="3.8">python</requirement> + <requirement type="package" version="2.20.1">requests</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Error downloading database." /> @@ -14,8 +16,18 @@ <command> <![CDATA[ #if $source.from == "uniprot" - #set $url = 'http://www.uniprot.org/uniprot/?query=taxonomy:"' + str($source.taxon) + '"' + str($source.set) + str($source.reviewed) + '&force=yes&format=fasta' + str($source.include_isoform) - #set $type = "direct" + #if $source.set: + #set $modified_set = '&' + str($source.set) + #else + #set $modified_set = '' + #end if + #if $source.taxon_id + #set $taxon_id = $source.taxon_id + #else + #set $taxon_id = $source.taxon + #end if + #set $url = 'https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=fasta&query=taxonomy_id:"' + str($taxon_id) + '"' + str($modified_set) + str($source.reviewed) + str($source.include_isoform) + #set $type = "uniprotkb_stream" #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" @@ -34,7 +46,9 @@ #set $url = $source.url #set $type = $source.archive_type #end if - #if $type =="direct" + #if $type =="uniprotkb_stream" + python '$__tool_directory__/uniprotkb.py' --url '$url' -o 'tmp.gz' && gzip -dc 'tmp.gz' > '${output_database}' + #elif $type =="direct" wget -nv '$url' -O '${output_database}' --no-check-certificate #elif $type =="zip" wget -nv '$url' -O tmp.zip --no-check-certificate && zcat -c tmp.zip > '${output_database}' @@ -51,7 +65,8 @@ </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 cross species collection of functional protein databases"> + <param name="from" type="select" label="Download from" + help="Select database source. cRAP acts as a database for common MS contaminants. UniProtKB is a cross species collection of functional protein databases"> <option value="uniprot">UniProtKB</option> <option value="cRAP">cRAP (contaminants)</option> <option value="HMP">Human Microbiome Project body sites</option> @@ -64,12 +79,14 @@ <options from_file="uniprot_taxons.loc"> <column name="name" index="0" /> <column name="value" index="1" /> + <filter type="add_value" name="Escherichia coli (strain K12)" value="83333" /> </options> </param> + <param name="taxon_id" type="integer" value="" min="1" optional="true" help="Specify a NCBI taxon id to override species selection"/> <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> + <option value="">UniProtKB</option> + <option value="+reviewed%3Atrue">UniProtKB/Swiss-Prot (reviewed only)</option> + <option value="+reviewed%3Afalse">UniProtKB/TrEMBL (unreviewed only)</option> <sanitizer> <valid> <add value="%"/> @@ -77,15 +94,16 @@ </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="">Any</option> + <option value="keyword%3aKW-1185" selected="true">Reference 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" /> + <param name="include_isoform" type="boolean" truevalue="&includeIsoform=true" falsevalue="" + label="Include isoform data" help="several different forms of a given protein are incorporated into database" /> </when> <when value="cRAP" /> <when value="HMP"> @@ -129,7 +147,9 @@ </outputs> <tests> <test> - <param name="from" value="cRAP" /> + <conditional name="source"> + <param name="from" value="cRAP" /> + </conditional> <output name="output_database"> <assert_contents> <has_text text="KKA1_ECOLX" /> @@ -137,6 +157,47 @@ </output> </test> <test> + <conditional name="source"> + <param name="from" value="uniprot" /> + <param name="taxon" value="83333"/> + <param name="taxon_id" value="2697049"/> + </conditional> + <output name="output_database"> + <assert_contents> + <has_text text="SPIKE_SARS2" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="source"> + <param name="from" value="uniprot" /> + <param name="taxon_id" value="2697049"/> + <param name="reviewed" value="+reviewed%3Atrue"/> + <param name="set" value=""/> + </conditional> + <output name="output_database"> + <assert_contents> + <has_text text=">sp|P0DTC1|R1A_SARS2" /> + <not_has_text text=">tr|A0A679G4D8|A0A679G4D8_SARS2" /> + </assert_contents> + </output> + </test> + <test> + <conditional name="source"> + <param name="from" value="uniprot" /> + <param name="taxon_id" value="2697049"/> + <param name="reviewed" value="+reviewed%3Afalse"/> + <param name="set" value=""/> + </conditional> + <output name="output_database"> + <assert_contents> + <has_text text=">tr|A0A679G4D8|A0A679G4D8_SARS2" /> + <not_has_text text=">sp|P0DTC1|R1A_SARS2" /> + </assert_contents> + </output> + </test> + + <test> <param name="from" value="url" /> <param name="url" value="https://raw.githubusercontent.com/pravs3683/cRAP/master/cRAP_protein_database.fasta" /> <param name="archive_type" value="direct" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/uniprotkb.py Tue Sep 27 13:22:04 2022 +0000 @@ -0,0 +1,30 @@ +#!/usr/bin/env python + +import argparse +import sys + +import requests + +uniprotkb_url = 'https://rest.uniprot.org/uniprotkb/stream?compressed=true&format=fasta&query=' + + +def __main__(): + parser = argparse.ArgumentParser( + description='Retrieve Uniprot data using streaming') + parser.add_argument('-u', '--url', help="Uniprot rest api URL") + parser.add_argument('-q', '--query', help="UniprotKB Query") + parser.add_argument('-o', '--output', type=argparse.FileType('wb'), default=sys.stdout, help='data') + parser.add_argument('-d', '--debug', action='store_true', help='Debug') + args = parser.parse_args() + if args.url: + url = args.url + else: + url = uniprotkb_url + args.query + with requests.get(url, stream=True) as request: + request.raise_for_status() + for chunk in request.iter_content(chunk_size=2**20): + args.output.write(chunk) + + +if __name__ == "__main__": + __main__()