# HG changeset patch
# User galaxyp
# Date 1368196810 14400
# Node ID e5ab158e482bece1aca255719b7a59aade300c7a
Initial upload.
diff -r 000000000000 -r e5ab158e482b LICENSE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Fri May 10 10:40:10 2013 -0400
@@ -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.
diff -r 000000000000 -r e5ab158e482b README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri May 10 10:40:10 2013 -0400
@@ -0,0 +1,25 @@
+The repository contains the tool wrapper for the TINT MGF
+formatter. This produces specially formatted MGF files for picky
+applications such as ProteinPilot and ms2preproc.
+# 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.
diff -r 000000000000 -r e5ab158e482b README_GALAXYP.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_GALAXYP.md Fri May 10 10:40:10 2013 -0400
@@ -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.
diff -r 000000000000 -r e5ab158e482b README_REPO.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md Fri May 10 10:40:10 2013 -0400
@@ -0,0 +1,3 @@
+The repository contains the tool wrapper for the TINT MGF
+formatter. This produces specially formatted MGF files for picky
+applications such as ProteinPilot and ms2preproc.
diff -r 000000000000 -r e5ab158e482b mgf_formatter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mgf_formatter.xml Fri May 10 10:40:10 2013 -0400
@@ -0,0 +1,45 @@
+
+ convert peak lists into MGF files formatted for particular downstream applications.
+
+
+ MgfFormatter --mgf_format $mgf_format --output '$output' $itraq_filter
+ #if $type.input_type == "mgf"
+ $type.split_multiple_charge_states
+ #end if
+ $type.inputs
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ tint_proteomics_scripts
+
+
+
+
diff -r 000000000000 -r e5ab158e482b repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Fri May 10 10:40:10 2013 -0400
@@ -0,0 +1,5 @@
+
+
+
+
+
diff -r 000000000000 -r e5ab158e482b tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri May 10 10:40:10 2013 -0400
@@ -0,0 +1,6 @@
+
+
+
+
+
+
diff -r 000000000000 -r e5ab158e482b update.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh Fri May 10 10:40:10 2013 -0400
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+LICENSE_FILE=LICENSE
+# Ensure repository contains license file.
+if [ ! -e "$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