changeset 5:4c820e82d22c

Uploaded
author galaxyp
date Fri, 26 Sep 2014 15:03:14 -0400
parents c29bb2fabcac
children b3cf7d7dadc1
files COPYING LICENSE README.md README_GALAXYP.md README_REPO.md convert_windows_newlines.xml proteinpilot_tabular.xml proteinpilot_xml.xml repository_dependencies.xml update.sh
diffstat 10 files changed, 185 insertions(+), 284 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Fri Sep 26 15:03:14 2014 -0400
@@ -0,0 +1,121 @@
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+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
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--- a/README.md	Thu Jun 20 16:20:32 2013 -0400
+++ b/README.md	Fri Sep 26 15:03:14 2014 -0400
@@ -1,23 +1,52 @@
-TODO: Document this tool repository.
-# Obtaining Tools
+GalaxyP - ProteinPilot
+======================
+
+* Home: <https://bitbucket.org/galaxyp/proteinpilot>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/proteinpilot>
+* Tool ID: `proteinpilot`
+
+
+Description
+-----------
+
+ProteinPilot
 
-Repositories for all Galaxy-P tools can be found at
-https:/bitbucket.org/galaxyp/.
+See:
+
+* <http://www.absciex.com/products/software/proteinpilot-software>
+
 
-# Contact
+GalaxyP Community
+-----------------
 
-Please send suggestions for improvements and bug reports to
-jmchilton@gmail.com.
+Current governing community policies for [GalaxyP](https://bitbucket.org/galaxyp/) and other information can be found at:
+
+<https://bitbucket.org/galaxyp/galaxyp>
+
 
-# License
+License
+-------
+
+Copyright (c) 2014 Regents of the University of Minnesota and Authors listed below.
 
-All Galaxy-P tools are licensed under the Apache License Version 2.0
-unless otherwise documented.
+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.
+
+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:
+
+* Cody Wang
+* John Chilton <jmchilton@gmail.com>
+* Minnesota Supercomputing Institute, Univeristy of Minnesota
--- a/README_GALAXYP.md	Thu Jun 20 16:20:32 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	Thu Jun 20 16:20:32 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-# proteinpilot
-
-Tools for working with ProteinPilot. ProteinPilot only runs on Windows
-machines and will require the use of the LWR job runner
-(https://bitbucket.org/jmchilton/lwr).
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_windows_newlines.xml	Fri Sep 26 15:03:14 2014 -0400
@@ -0,0 +1,15 @@
+<tool id="convert_windows_newlines" version="0.1" name="ProteinPilot - Convert Windows Line Breaks">
+  <description></description>
+  <command>
+     tr -d '\r' &lt; $input1  &gt; $output
+  </command>
+  <inputs>
+    <param format="txt" name="input1" type="data" label="Tabular Input File" help=""/>
+  </inputs>
+  <outputs>
+    <data name="output" format="input" metadata_source="input1"/>
+  </outputs>
+  <help>
+    Standardize the output of Windows tools like "Convert ProteinPilot Group to Tabular" for use in Galaxy.
+  </help>
+</tool>
--- a/proteinpilot_tabular.xml	Thu Jun 20 16:20:32 2013 -0400
+++ b/proteinpilot_tabular.xml	Fri Sep 26 15:03:14 2014 -0400
@@ -1,5 +1,6 @@
-<tool id="proteinpilot_tabular" version="0.1" name="Convert ProteinPilot Group to Tabular">
+<tool id="proteinpilot_tabular" version="0.1" name="ProteinPilot - Convert Group to Tabular">
   <description></description>
+  <!-- TOOD: Implement wrapper allowing Windows newlines to be replaced. -->
   <command>
     #if $quant.use
     #set $denom = $quant.type
--- a/proteinpilot_xml.xml	Thu Jun 20 16:20:32 2013 -0400
+++ b/proteinpilot_xml.xml	Fri Sep 26 15:03:14 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="proteinpilot_xml" version="0.1" name="Convert ProteinPilot Group to XML">
+<tool id="proteinpilot_xml" version="0.1" name="ProteinPilot - Convert Group to XML">
   <description></description>
   <command>
     group2xml.exe XML $input $output
--- a/repository_dependencies.xml	Thu Jun 20 16:20:32 2013 -0400
+++ b/repository_dependencies.xml	Fri Sep 26 15:03:14 2014 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Required proteomics dependencies.">
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc" />
+  <repository changeset_revision="f66f8ca7b7b9" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
--- a/update.sh	Thu Jun 20 16:20:32 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-#!/bin/bash
-
-LICENSE_FILE=LICENSE
-# Ensure repository contains license file.
-if [ ! -e "$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