Mercurial > repos > galaxyp > dbbuilder
changeset 0:487f80fb99ae draft
Uploaded
author | galaxyp |
---|---|
date | Wed, 19 Dec 2012 00:05:32 -0500 |
parents | |
children | abbd37e8bd14 |
files | LICENSE README.md README_GALAXYP.md README_REPO.md dbbuilder.xml update.sh |
diffstat | 6 files changed, 335 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed Dec 19 00:05:32 2012 -0500 @@ -0,0 +1,202 @@ + + 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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Dec 19 00:05:32 2012 -0500 @@ -0,0 +1,26 @@ +# Protein Database Downloader + +This tool allows users to download protein databases from common +sources. This tool has no external dependencies beyond wget. +# 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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_GALAXYP.md Wed Dec 19 00:05:32 2012 -0500 @@ -0,0 +1,22 @@ +# 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.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Wed Dec 19 00:05:32 2012 -0500 @@ -0,0 +1,4 @@ +# Protein Database Downloader + +This tool allows users to download protein databases from common +sources. This tool has no external dependencies beyond wget.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dbbuilder.xml Wed Dec 19 00:05:32 2012 -0500 @@ -0,0 +1,46 @@ +<tool id="dbbuilder" version="0.1.0" name="Protein Database Downloader"> + <description> + </description> + <requirements> + <requirement type="binary">wget</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Error computing FDR" /> + </stdio> + <command> + #if $source.from == "uniprot" + #set $url = "http://www.uniprot.org/uniprot/?query=taxonomy%3a%22" + str($source.taxon) + "%22+keyword%3a1185&force=yes&format=fasta" + str($source.include_isoform) + #elif $source.from == "cRAP" + #set $url = "ftp://ftp.thegpm.org/fasta/cRAP/crap.fasta" + #end if + wget -nv '$url' -O '${output_database}' + </command> + <inputs> + <conditional name="source"> + <param name="from" type="select" label="Download from"> + <option value="uniprot">UniProtKB</option> + <option value="cRAP">cRAP (contaminants)</option> + </param> + <when value="uniprot"> + <param name="taxon" type="select" format="text" > + <label>Taxonomy</label> + <options from_file="uniprot_taxons.loc"> + <column name="name" index="0" /> + <column name="value" index="1" /> + </options> + </param> + <param name="include_isoform" type="boolean" truevalue="&include=yes" falsevalue="" label="Include isoform data" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="fasta" name="output_database" label="Protein Database" /> + </outputs> + <help> +**Output** + +A FASTA file containing the specified protein sequences. + + </help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Wed Dec 19 00:05:32 2012 -0500 @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$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