Mercurial > repos > galaxyp > dbbuilder
changeset 0:ab1148688233 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dbbuilder commit da321d452c314c8c66ea848fe1fe20879c03b0e4
| author | galaxyp |
|---|---|
| date | Sat, 29 Apr 2017 09:46:11 -0400 |
| parents | |
| children | a2c05481cae2 |
| files | COPYING README.md dbbuilder.xml test-data/.gitkeep tool-data/uniprot_taxons.loc.sample |
| diffstat | 4 files changed, 298 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Sat Apr 29 09:46:11 2017 -0400 @@ -0,0 +1,48 @@ +GalaxyP - Protein Database Downloader +===================================== + +* Home: <https://github.com/galaxyproteomics/tools-galaxyp/> +* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/dbbuilder> +* Tool ID: `dbbuilder` + + +Description +----------- + +Download protein databases from common sources. + + +GalaxyP Community +----------------- + +Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at: + +<https://github.com/galaxyproteomics> + + +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. + +To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty. + +You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>. + +You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. + + +Contributing +------------ + +Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/> + + +Authors +------- + +Authors and contributors: + +* Fred Sadler +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dbbuilder.xml Sat Apr 29 09:46:11 2017 -0400 @@ -0,0 +1,109 @@ +<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> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/uniprot_taxons.loc.sample Sat Apr 29 09:46:11 2017 -0400 @@ -0,0 +1,20 @@ +Homo sapiens (Human) 9606 +Rattus norvegicus (Rat) 10116 +Mus musculus (Mouse) 10090 +Bos taurus (Bovine) 9913 +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 +Canis familiaris (Dog) 9615 +Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 64091 +Apis mellifera (Honeybee) 7460 +Mycobacterium tuberculosis H37Rv (MTB) [Not complete proteome] 83332 +Mycoplasma orale [Not complete proteome] 2121 +Mycoplasma hyorhinis 2100 +Mycoplasma arginini 2094 +Mycoplasma fermentans 2115 +Mycoplasma hominis 2098 +Acholeplasma laidlawii 2148