changeset 0:44077d92c836 draft

Initial commit.
author galaxyp
date Thu, 09 May 2013 17:14:17 -0400
parents
children 437a18ccbdc2
files LICENSE README.md README_GALAXYP.md README_REPO.md iquant.xml repository_dependencies.xml tool_dependencies.xml update.sh
diffstat 8 files changed, 363 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE	Thu May 09 17:14:17 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.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,23 @@
+TODO: Document this tool repository.
+# 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	Thu May 09 17:14:17 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.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README_REPO.md	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,1 @@
+TODO: Document this tool repository.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iquant.xml	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,69 @@
+<tool id="iquant" name="iQuant" version="0.2.0">
+  <description>Perform quantitation on data labeled with isobaric tags.</description>
+  <command>
+    LTQ-iQuant-cli --report_type ${peptide_report.report_type} --group_type ${group_type} --report ${peptide_report.report} --type ${quant_type} --output $output
+    #for $input in $inputs:
+    "${input}"
+    #end for
+  </command>
+  <inputs>
+    <conditional name="peptide_report">
+      <param name="report_type" type="select" label="Identification Report Type">
+        <option value="PEPXML">PepXML</option>
+        <option value="SCAFFOLD">Scaffold Spectrum Report</option>
+        <option value="PROTEIN_PILOT">ProteinPilot Peptide Report</option>
+        <option value="MAX_QUANT">MaxQuant MSMS Export</option>
+      </param>
+      <when value="PEPXML">
+        <param format="pepxml" name="report" type="data" label="Input PepXML"/>
+      </when>
+      <when value="SCAFFOLD">
+        <param format="text" name="report" type="data" label="Input Scaffold Report"/>
+      </when>
+      <when value="PROTEIN_PILOT">
+        <param format="text" name="report" type="data" label="Input ProteinPilot Peptide Report"/>
+      </when>
+      <when value="MAX_QUANT">
+        <param format="text" name="report" type="data" label="Input MaxQuant MSMS Export"/>
+      </when>
+    </conditional>
+    <param name="inputs" multiple="true" type="data" format="mzxml,mzml" label="Peaklist(s)" help=""/>
+    <param name="quant_type" type="select" label="Quantification type">
+      <option value="FOUR_PLEX">iTRAQ 4-plex</option>
+      <option value="EIGHT_PLEX">iTRAQ 8-plex</option>
+      <option value="TMT_TWO_PLEX">TMT 2-plex</option>
+      <option value="TMT_SIX_PLEX">TMT 6-plex</option>
+    </param>
+    <param name="group_type" type="select" label="Quantify based on grouping of">
+      <option value="PROTEIN">Proteins</option>
+      <option value="PEPTIDE">Peptides</option>
+      <option value="PEPTIDE_WITH_MODIFICATIONS">Peptides with modifications</option>
+      <option value="PEPTIDE_WITH_UNIQUE_MODIFICATION">Peptide with an identified modification</option>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+
+  <requirements>
+    <requirement type="package" version="1.19.19">tint_proteomics_scripts</requirement><!-- Version 1.19.19 or higher -->
+  </requirements>
+
+  <help>
+**What it does**
+
+iQuant is a tool that performs tag based isobaric quantification by implementing a technique assigning collective reporter ion intensity-based weights to each peptide abundance ratio and calculating a protein's weighted average abundance ratio and p-value. 
+
+iQuant requires identification results from an upstream identification pipeline along with XML peak lists for the data (mzXML is well supported and an mzML option has been provided for testing). 
+
+------
+
+**Citation**
+
+For the underlying tool, please cite ``Onsongo G, Stone MD, Van Riper SK, Chilton J, Wu B, Higgins L, Lund TC, Carlis JV, Griffin TJ, 2010. LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments. Proteomics. 10(19).  doi: 10.1002/pmic.201000189.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-iquant
+
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<repositories description="Required proteomics dependencies.">
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tint" owner="galaxyp" changeset_revision="ab43b5ba7a4e"/>
+  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc" />
+</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu May 09 17:14:17 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="tint_proteomics_scripts" version="1.19.19">
+    <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tint" owner="galaxyp" changeset_revision="ab43b5ba7a4e"/>
+  </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/update.sh	Thu May 09 17:14:17 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