# HG changeset patch # User galaxyp # Date 1411758634 14400 # Node ID 0d0cbb69a03fd862eedd7cadfa5e4787c7fd8393 # Parent e9981e6af6668304ce93b6f2accd00dec872d9a2 Uploaded diff -r e9981e6af666 -r 0d0cbb69a03f COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Sep 26 15:10:34 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. 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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 . + +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 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: + +* John Chilton +* Minnesota Supercomputing Institute, Univeristy of Minnesota diff -r e9981e6af666 -r 0d0cbb69a03f README_GALAXYP.md --- a/README_GALAXYP.md Thu Jun 20 11:07:47 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. diff -r e9981e6af666 -r 0d0cbb69a03f README_REPO.md --- a/README_REPO.md Thu Jun 20 11:07:47 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -Tool wrapper for the commercial proteomics application Scaffold. diff -r e9981e6af666 -r 0d0cbb69a03f macros.xml --- a/macros.xml Thu Jun 20 11:07:47 2013 -0400 +++ b/macros.xml Fri Sep 26 15:10:34 2014 -0400 @@ -27,4 +27,4 @@ - \ No newline at end of file + diff -r e9981e6af666 -r 0d0cbb69a03f scaffold.xml --- a/scaffold.xml Thu Jun 20 11:07:47 2013 -0400 +++ b/scaffold.xml Fri Sep 26 15:10:34 2014 -0400 @@ -7,10 +7,10 @@ #if $sample_mode.mode == "full" #set $samples = $sample_mode.samples #for $sample in $samples: -#if $sample.category.specify +#if $sample.category.specify #set $category = $sample.category.name #else -#set $category = $sample.sample_name +#set $category = $sample.sample_name #end if sample:$sample.sample_name mudpit:$sample.mudpit @@ -47,7 +47,7 @@ #end if #if $advanced.specify #if $advanced.output_driver - --output_driver $output_drirver \ + --output_driver $output_driver \ #end if #end if @@ -87,7 +87,7 @@ - + @@ -114,7 +114,7 @@ - + (advanced['specify'] and advanced["output_driver"]) @@ -134,6 +134,6 @@ For the underlying tool, please cite `TODO` -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-scaffold +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/scaffold - \ No newline at end of file + diff -r e9981e6af666 -r 0d0cbb69a03f scaffold_export.xml --- a/scaffold_export.xml Thu Jun 20 11:07:47 2013 -0400 +++ b/scaffold_export.xml Fri Sep 26 15:10:34 2014 -0400 @@ -70,6 +70,6 @@ For the underlying tool, please cite `TODO` -If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-scaffold +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/scaffold - \ No newline at end of file + diff -r e9981e6af666 -r 0d0cbb69a03f scaffold_wrapper.py --- a/scaffold_wrapper.py Thu Jun 20 11:07:47 2013 -0400 +++ b/scaffold_wrapper.py Fri Sep 26 15:10:34 2014 -0400 @@ -47,8 +47,8 @@ if returncode != 0: raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())) finally: - print open(tmp_stderr_name, "r").read(64000) - print open(tmp_stdout_name, "r").read(64000) + print((open(tmp_stderr_name, "r").read(64000))) + print((open(tmp_stdout_name, "r").read(64000))) def delete_file(path): @@ -152,7 +152,7 @@ def build_samples(samples_file): group_data = parse_groups(samples_file, group_parts=["sample", "mudpit", "category"], input_parts=["name", "path", "ext"]) samples_description = "" - for sample_name, sample_data in group_data.iteritems(): + for sample_name, sample_data in list(group_data.items()): files = sample_data["inputs"] mudpit = sample_data["group_data"]["mudpit"] category = sample_data["group_data"]["category"] @@ -307,7 +307,7 @@ # Prepare and create driver file driver_contents = Template(template).substitute(template_parameters) - print driver_contents + print(driver_contents) driver_path = os.path.abspath("driver.xml") open(driver_path, "w").write(driver_contents) diff -r e9981e6af666 -r 0d0cbb69a03f update.sh --- a/update.sh Thu Jun 20 11:07:47 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