Mercurial > repos > galaxyp > dbbuilder
changeset 4:b39347891609 draft
Uploaded
| author | galaxyp |
|---|---|
| date | Fri, 26 Sep 2014 14:31:06 -0400 |
| parents | a38cd98a6b41 |
| children | 1d3557cec567 |
| files | COPYING LICENSE README.md README_GALAXYP.md README_REPO.md dbbuilder.xml test-data/.gitkeep tool-data/uniprot_taxons.loc.sample tools/dbbuilder.xml uniprot_taxons.loc.sample update.sh |
| diffstat | 10 files changed, 270 insertions(+), 390 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Sep 26 14:31:06 2014 -0400 @@ -0,0 +1,121 @@ +Creative Commons Legal Code + +CC0 1.0 Universal + + CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE + LEGAL SERVICES. DISTRIBUTION OF THIS DOCUMENT DOES NOT CREATE AN + ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS + INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES + REGARDING THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS + PROVIDED HEREUNDER, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM + THE USE OF THIS DOCUMENT OR THE INFORMATION OR WORKS PROVIDED + HEREUNDER. + +Statement of Purpose + +The laws of most jurisdictions throughout the world automatically confer +exclusive Copyright and Related Rights (defined below) upon the creator +and subsequent owner(s) (each and all, an "owner") of an original work of +authorship and/or a database (each, a "Work"). + +Certain owners wish to permanently relinquish those rights to a Work for +the purpose of contributing to a commons of creative, cultural and +scientific works ("Commons") that the public can reliably and without fear +of later claims of infringement build upon, modify, incorporate in other +works, reuse and redistribute as freely as possible in any form whatsoever +and for any purposes, including without limitation commercial purposes. +These owners may contribute to the Commons to promote the ideal of a free +culture and the further production of creative, cultural and scientific +works, or to gain reputation or greater distribution for their Work in +part through the use and efforts of others. + +For these and/or other purposes and motivations, and without any +expectation of additional consideration or compensation, the person +associating CC0 with a Work (the "Affirmer"), to the extent that he or she +is an owner of Copyright and Related Rights in the Work, voluntarily +elects to apply CC0 to the Work and publicly distribute the Work under its +terms, with knowledge of his or her Copyright and Related Rights in the +Work and the meaning and intended legal effect of CC0 on those rights. + +1. Copyright and Related Rights. A Work made available under CC0 may be +protected by copyright and related or neighboring rights ("Copyright and +Related Rights"). Copyright and Related Rights include, but are not +limited to, the following: + + i. the right to reproduce, adapt, distribute, perform, display, + communicate, and translate a Work; + ii. moral rights retained by the original author(s) and/or performer(s); +iii. publicity and privacy rights pertaining to a person's image or + likeness depicted in a Work; + iv. rights protecting against unfair competition in regards to a Work, + subject to the limitations in paragraph 4(a), below; + v. rights protecting the extraction, dissemination, use and reuse of data + in a Work; + vi. database rights (such as those arising under Directive 96/9/EC of the + European Parliament and of the Council of 11 March 1996 on the legal + protection of databases, and under any national implementation + thereof, including any amended or successor version of such + directive); and +vii. other similar, equivalent or corresponding rights throughout the + world based on applicable law or treaty, and any national + implementations thereof. + +2. Waiver. To the greatest extent permitted by, but not in contravention +of, applicable law, Affirmer hereby overtly, fully, permanently, +irrevocably and unconditionally waives, abandons, and surrenders all of +Affirmer's Copyright and Related Rights and associated claims and causes +of action, whether now known or unknown (including existing as well as +future claims and causes of action), in the Work (i) in all territories +worldwide, (ii) for the maximum duration provided by applicable law or +treaty (including future time extensions), (iii) in any current or future +medium and for any number of copies, and (iv) for any purpose whatsoever, +including without limitation commercial, advertising or promotional +purposes (the "Waiver"). Affirmer makes the Waiver for the benefit of each +member of the public at large and to the detriment of Affirmer's heirs and +successors, fully intending that such Waiver shall not be subject to +revocation, rescission, cancellation, termination, or any other legal or +equitable action to disrupt the quiet enjoyment of the Work by the public +as contemplated by Affirmer's express Statement of Purpose. + +3. Public License Fallback. Should any part of the Waiver for any reason +be judged legally invalid or ineffective under applicable law, then the +Waiver shall be preserved to the maximum extent permitted taking into +account Affirmer's express Statement of Purpose. In addition, to the +extent the Waiver is so judged Affirmer hereby grants to each affected +person a royalty-free, non transferable, non sublicensable, non exclusive, +irrevocable and unconditional license to exercise Affirmer's Copyright and +Related Rights in the Work (i) in all territories worldwide, (ii) for the +maximum duration provided by applicable law or treaty (including future +time extensions), (iii) in any current or future medium and for any number +of copies, and (iv) for any purpose whatsoever, including without +limitation commercial, advertising or promotional purposes (the +"License"). The License shall be deemed effective as of the date CC0 was +applied by Affirmer to the Work. Should any part of the License for any +reason be judged legally invalid or ineffective under applicable law, such +partial invalidity or ineffectiveness shall not invalidate the remainder +of the License, and in such case Affirmer hereby affirms that he or she +will not (i) exercise any of his or her remaining Copyright and Related +Rights in the Work or (ii) assert any associated claims and causes of +action with respect to the Work, in either case contrary to Affirmer's +express Statement of Purpose. + +4. Limitations and Disclaimers. + + a. No trademark or patent rights held by Affirmer are waived, abandoned, + surrendered, licensed or otherwise affected by this document. + b. Affirmer offers the Work as-is and makes no representations or + warranties of any kind concerning the Work, express, implied, + statutory or otherwise, including without limitation warranties of + title, merchantability, fitness for a particular purpose, non + infringement, or the absence of latent or other defects, accuracy, or + the present or absence of errors, whether or not discoverable, all to + the greatest extent permissible under applicable law. + c. Affirmer disclaims responsibility for clearing rights of other persons + that may apply to the Work or any use thereof, including without + limitation any person's Copyright and Related Rights in the Work. + Further, Affirmer disclaims responsibility for obtaining any necessary + consents, permissions or other rights required for any use of the + Work. + d. Affirmer understands and acknowledges that Creative Commons is not a + party to this document and has no duty or obligation with respect to + this CC0 or use of the Work.
--- a/LICENSE Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,202 +0,0 @@ - - Apache License - Version 2.0, January 2004 - http://www.apache.org/licenses/ - - TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION - - 1. Definitions. - - "License" shall mean the terms and conditions for use, reproduction, - and distribution as defined by Sections 1 through 9 of this document. - - "Licensor" shall mean the copyright owner or entity authorized by - the copyright owner that is granting the License. - - "Legal Entity" shall mean the union of the acting entity and all - other entities that control, are controlled by, or are under common - control with that entity. For the purposes of this definition, - "control" means (i) the power, direct or indirect, to cause the - direction or management of such entity, whether by contract or - otherwise, or (ii) ownership of fifty percent (50%) or more of the - outstanding shares, or (iii) beneficial ownership of such entity. - - "You" (or "Your") shall mean an individual or Legal Entity - exercising permissions granted by this License. - - "Source" form shall mean the preferred form for making modifications, - including but not limited to software source code, documentation - source, and configuration files. - - "Object" form shall mean any form resulting from mechanical - transformation or translation of a Source form, including but - not limited to compiled object code, generated documentation, - and conversions to other media types. - - "Work" shall mean the work of authorship, whether in Source or - Object form, made available under the License, as indicated by a - copyright notice that is included in or attached to the work - (an example is provided in the Appendix below). - - "Derivative Works" shall mean any work, whether in Source or Object - form, that is based on (or derived from) the Work and for which the - editorial revisions, annotations, elaborations, or other modifications - represent, as a whole, an original work of authorship. For the purposes - of this License, Derivative Works shall not include works that remain - separable from, or merely link (or bind by name) to the interfaces of, - the Work and Derivative Works thereof. - - "Contribution" shall mean any work of authorship, including - the original version of the Work and any modifications or additions - to that Work or Derivative Works thereof, that is intentionally - submitted to Licensor for inclusion in the Work by the copyright owner - or by an individual or Legal Entity authorized to submit on behalf of - the copyright owner. For the purposes of this definition, "submitted" - means any form of electronic, verbal, or written communication sent - to the Licensor or its representatives, including but not limited to - communication on electronic mailing lists, source code control systems, - and issue tracking systems that are managed by, or on behalf of, the - Licensor for the purpose of discussing and improving the Work, but - excluding communication that is conspicuously marked or otherwise - designated in writing by the copyright owner as "Not a Contribution." - - "Contributor" shall mean Licensor and any individual or Legal Entity - on behalf of whom a Contribution has been received by Licensor and - subsequently incorporated within the Work. - - 2. Grant of Copyright License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - copyright license to reproduce, prepare Derivative Works of, - publicly display, publicly perform, sublicense, and distribute the - Work and such Derivative Works in Source or Object form. - - 3. Grant of Patent License. Subject to the terms and conditions of - this License, each Contributor hereby grants to You a perpetual, - worldwide, non-exclusive, no-charge, royalty-free, irrevocable - (except as stated in this section) patent license to make, have made, - use, offer to sell, sell, import, and otherwise transfer the Work, - where such license applies only to those patent claims licensable - by such Contributor that are necessarily infringed by their - Contribution(s) alone or by combination of their Contribution(s) - with the Work to which such Contribution(s) was submitted. If You - institute patent litigation against any entity (including a - cross-claim or counterclaim in a lawsuit) alleging that the Work - or a Contribution incorporated within the Work constitutes direct - or contributory patent infringement, then any patent licenses - granted to You under this License for that Work shall terminate - as of the date such litigation is filed. - - 4. Redistribution. You may reproduce and distribute copies of the - Work or Derivative Works thereof in any medium, with or without - modifications, and in Source or Object form, provided that You - meet the following conditions: - - (a) You must give any other recipients of the Work or - Derivative Works a copy of this License; and - - (b) You must cause any modified files to carry prominent notices - stating that You changed the files; and - - (c) You must retain, in the Source form of any Derivative Works - that You distribute, all copyright, patent, trademark, and - attribution notices from the Source form of the Work, - excluding those notices that do not pertain to any part of - the Derivative Works; and - - (d) If the Work includes a "NOTICE" text file as part of its - distribution, then any Derivative Works that You distribute must - include a readable copy of the attribution notices contained - within such NOTICE file, excluding those notices that do not - pertain to any part of the Derivative Works, in at least one - of the following places: within a NOTICE text file distributed - as part of the Derivative Works; within the Source form or - documentation, if provided along with the Derivative Works; or, - within a display generated by the Derivative Works, if and - wherever such third-party notices normally appear. The contents - of the NOTICE file are for informational purposes only and - do not modify the License. You may add Your own attribution - notices within Derivative Works that You distribute, alongside - or as an addendum to the NOTICE text from the Work, provided - that such additional attribution notices cannot be construed - as modifying the License. - - You may add Your own copyright statement to Your modifications and - may provide additional or different license terms and conditions - for use, reproduction, or distribution of Your modifications, or - for any such Derivative Works as a whole, provided Your use, - reproduction, and distribution of the Work otherwise complies with - the conditions stated in this License. - - 5. Submission of Contributions. Unless You explicitly state otherwise, - any Contribution intentionally submitted for inclusion in the Work - by You to the Licensor shall be under the terms and conditions of - this License, without any additional terms or conditions. - Notwithstanding the above, nothing herein shall supersede or modify - the terms of any separate license agreement you may have executed - with Licensor regarding such Contributions. - - 6. Trademarks. This License does not grant permission to use the trade - names, trademarks, service marks, or product names of the Licensor, - except as required for reasonable and customary use in describing the - origin of the Work and reproducing the content of the NOTICE file. - - 7. Disclaimer of Warranty. Unless required by applicable law or - agreed to in writing, Licensor provides the Work (and each - Contributor provides its Contributions) on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or - implied, including, without limitation, any warranties or conditions - of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A - PARTICULAR PURPOSE. You are solely responsible for determining the - appropriateness of using or redistributing the Work and assume any - risks associated with Your exercise of permissions under this License. - - 8. Limitation of Liability. In no event and under no legal theory, - whether in tort (including negligence), contract, or otherwise, - unless required by applicable law (such as deliberate and grossly - negligent acts) or agreed to in writing, shall any Contributor be - liable to You for damages, including any direct, indirect, special, - incidental, or consequential damages of any character arising as a - result of this License or out of the use or inability to use the - Work (including but not limited to damages for loss of goodwill, - work stoppage, computer failure or malfunction, or any and all - other commercial damages or losses), even if such Contributor - has been advised of the possibility of such damages. - - 9. Accepting Warranty or Additional Liability. While redistributing - the Work or Derivative Works thereof, You may choose to offer, - and charge a fee for, acceptance of support, warranty, indemnity, - or other liability obligations and/or rights consistent with this - License. However, in accepting such obligations, You may act only - on Your own behalf and on Your sole responsibility, not on behalf - of any other Contributor, and only if You agree to indemnify, - defend, and hold each Contributor harmless for any liability - incurred by, or claims asserted against, such Contributor by reason - of your accepting any such warranty or additional liability. - - END OF TERMS AND CONDITIONS - - APPENDIX: How to apply the Apache License to your work. - - To apply the Apache License to your work, attach the following - boilerplate notice, with the fields enclosed by brackets "[]" - replaced with your own identifying information. (Don't include - the brackets!) The text should be enclosed in the appropriate - comment syntax for the file format. We also recommend that a - file or class name and description of purpose be included on the - same "printed page" as the copyright notice for easier - identification within third-party archives. - - Copyright [yyyy] [name of copyright owner] - - Licensed under the Apache License, Version 2.0 (the "License"); - you may not use this file except in compliance with the License. - You may obtain a copy of the License at - - http://www.apache.org/licenses/LICENSE-2.0 - - Unless required by applicable law or agreed to in writing, software - distributed under the License is distributed on an "AS IS" BASIS, - WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - See the License for the specific language governing permissions and - limitations under the License.
--- a/README.md Fri Jul 12 12:57:50 2013 -0400 +++ b/README.md Fri Sep 26 14:31:06 2014 -0400 @@ -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
--- a/README_GALAXYP.md Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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.
--- a/README_REPO.md Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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.
--- a/dbbuilder.xml Fri Jul 12 12:57:50 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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> -
--- /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 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/dbbuilder.xml Fri Sep 26 14:31:06 2014 -0400 @@ -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> +
--- 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
--- 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