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README.md |
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COPYING test-data/.gitkeep tool-data/uniprot_taxons.loc.sample tools/dbbuilder.xml |
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LICENSE README_GALAXYP.md README_REPO.md dbbuilder.xml uniprot_taxons.loc.sample update.sh |
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| diff -r a38cd98a6b41 -r b39347891609 COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Sep 26 14:31:06 2014 -0400 |
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| diff -r a38cd98a6b41 -r b39347891609 LICENSE --- a/LICENSE Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,202 +0,0 @@\n-\n- Apache License\n- Version 2.0, January 2004\n- http://www.apache.org/licenses/\n-\n- TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION\n-\n- 1. Definitions.\n-\n- "License" shall mean the terms and conditions for use, reproduction,\n- and distribution as defined by Sections 1 through 9 of this document.\n-\n- "Licensor" shall mean the copyright owner or entity authorized by\n- the copyright owner that is granting the License.\n-\n- "Legal Entity" shall mean the union of the acting entity and all\n- other entities that control, are controlled by, or are under common\n- control with that entity. 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| diff -r a38cd98a6b41 -r b39347891609 README.md --- a/README.md Fri Jul 12 12:57:50 2013 -0400 +++ b/README.md Fri Sep 26 14:31:06 2014 -0400 |
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| @@ -1,26 +1,48 @@ -# Protein Database Downloader +GalaxyP - Protein Database Downloader +===================================== + +* Home: <https://bitbucket.org/galaxyp/dbbuilder> +* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/dbbuilder> +* Tool ID: `dbbuilder` + + +Description +----------- -This tool allows users to download protein databases from common -sources. This tool has no external dependencies beyond wget. -# Obtaining Tools +Download protein databases from common sources. + -Repositories for all Galaxy-P tools can be found at -https:/bitbucket.org/galaxyp/. +GalaxyP Community +----------------- -# Contact +Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at: + +<https://bitbucket.org/galaxyp/galaxyp> + -Please send suggestions for improvements and bug reports to -jmchilton@gmail.com. +License +------- + +Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below. -# License +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. -All Galaxy-P tools are licensed under the Apache License Version 2.0 -unless otherwise documented. +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. + -# Tool Versioning +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://bitbucket.org/galaxyp/galaxyp/CONTRIBUTORS.md> unless you opt-out. + -Galaxy-P tools will have versions of the form X.Y.Z. Versions -differing only after the second decimal should be completely -compatible with each other. Breaking changes should result in an -increment of the number before and/or after the first decimal. All -tools of version less than 1.0.0 should be considered beta. +Authors +------- + +Authors and contributors: + +* Fred Sadler +* John Chilton <jmchilton@gmail.com> +* Minnesota Supercomputing Institute, Univeristy of Minnesota |
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| diff -r a38cd98a6b41 -r b39347891609 README_GALAXYP.md --- a/README_GALAXYP.md Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,22 +0,0 @@ -# Obtaining Tools - -Repositories for all Galaxy-P tools can be found at -https:/bitbucket.org/galaxyp/. - -# Contact - -Please send suggestions for improvements and bug reports to -jmchilton@gmail.com. - -# License - -All Galaxy-P tools are licensed under the Apache License Version 2.0 -unless otherwise documented. - -# Tool Versioning - -Galaxy-P tools will have versions of the form X.Y.Z. Versions -differing only after the second decimal should be completely -compatible with each other. Breaking changes should result in an -increment of the number before and/or after the first decimal. All -tools of version less than 1.0.0 should be considered beta. |
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| diff -r a38cd98a6b41 -r b39347891609 README_REPO.md --- a/README_REPO.md Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -# Protein Database Downloader - -This tool allows users to download protein databases from common -sources. This tool has no external dependencies beyond wget. |
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| diff -r a38cd98a6b41 -r b39347891609 dbbuilder.xml --- a/dbbuilder.xml Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,95 +0,0 @@ -<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 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" + 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" 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> - <help> -**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> - |
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| diff -r a38cd98a6b41 -r b39347891609 tool-data/uniprot_taxons.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/uniprot_taxons.loc.sample Fri Sep 26 14:31:06 2014 -0400 |
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| @@ -0,0 +1,14 @@ +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 |
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| diff -r a38cd98a6b41 -r b39347891609 tools/dbbuilder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/dbbuilder.xml Fri Sep 26 14:31:06 2014 -0400 |
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| @@ -0,0 +1,95 @@ +<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 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" + 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" 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> + <help> +**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> + |
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| diff -r a38cd98a6b41 -r b39347891609 uniprot_taxons.loc.sample --- a/uniprot_taxons.loc.sample Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,14 +0,0 @@ -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 |
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| diff -r a38cd98a6b41 -r b39347891609 update.sh --- a/update.sh Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,35 +0,0 @@ -#!/bin/bash - -LICENSE_FILE=LICENSE -# Ensure repository contains license file. -if [ ! -e "$LICENSE_FILE" ]; -then - wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE" -fi - -# Run repository specific update actions. -if [ -f update_repo.sh ]; -then - ./update_repo.sh -fi - -wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md - -# Create repository README -if [ ! -e README_REPO.md ]; -then - echo "TODO: Document this tool repository." > README_REPO.md -fi -cat README_REPO.md README_GALAXYP.md > README.md - - -# If version file exists, update all tools to this version -VERSION_FILE=version -if [ -e "$VERSION_FILE" ]; -then - VERSION=`cat $VERSION_FILE` - - # Replace tool version in each tool XML file ` - find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \; - -fi |