<commit_before><?xml version="1.0"?>

<tool_dependency>
    <package name="neptune" version="1.2.1">
        <install version="1.0">

            <actions>
                <action type="shell_command">git clone https://github.com/phac-nml/neptune.git</action>
				<action type="shell_command">git checkout release/1.2</action>

				<action type="move_directory_files">
					<source_directory>neptune</source_directory>
					<destination_directory>$INSTALL_DIR/neptune</destination_directory>
				</action>

                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/neptune</environment_variable>
                </action>
            </actions>
        </install>
        <readme>

# Neptune #
-----------

## Legal ##
-----------

Neptune

Copyright Government of Canada 2015-2016

Written by: <NAME>, Public Health Agency of Canada,
    National Microbiology Laboratory

Funded by the National Micriobiology Laboratory and the Genome Canada / Alberta
    Innovates Bio Solutions project "Listeria Detection and Surveillance
    using Next Generation Genomics"

Licensed under the Apache License, Version 2.0 (the "License"); you may not use
this work 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.

## Description ##
-----------------

Neptune locates genomic signatures using an exact k-mer matching strategy while
accommodating k-mer mismatches. The software identifies sequences that are
sufficiently represented within inclusion targets and sufficiently absent from
exclusion targets. The signature discovery process is accomplished using
probabilistic models instead of heuristic strategies.

## Release ##
-------------

**Neptune 1.2.1**

2016 March 18

This release of Neptune allows for execution on a single machine without
requiring DRMAA. Furthermore, several command line parameters have been
modified.

## Requirements ##<commit_msg>Updated README section: release.<commit_after><?xml version="1.0"?>

<tool_dependency>
    <package name="neptune" version="1.2.1">
        <install version="1.0">

            <actions>
                <action type="shell_command">git clone https://github.com/phac-nml/neptune.git</action>
				<action type="shell_command">git checkout release/1.2</action>

				<action type="move_directory_files">
					<source_directory>neptune</source_directory>
					<destination_directory>$INSTALL_DIR/neptune</destination_directory>
				</action>

                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/neptune</environment_variable>
                </action>
            </actions>
        </install>
        <readme>

# Neptune #
-----------

## Legal ##
-----------

Neptune

Copyright Government of Canada 2015-2016

Written by: <NAME>, Public Health Agency of Canada,
    National Microbiology Laboratory

Funded by the National Micriobiology Laboratory and the Genome Canada / Alberta
    Innovates Bio Solutions project "Listeria Detection and Surveillance
    using Next Generation Genomics"

Licensed under the Apache License, Version 2.0 (the "License"); you may not use
this work 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.

## Description ##
-----------------

Neptune locates genomic signatures using an exact k-mer matching strategy while
accommodating k-mer mismatches. The software identifies sequences that are
sufficiently represented within inclusion targets and sufficiently absent from
exclusion targets. The signature discovery process is accomplished using
probabilistic models instead of heuristic strategies.

## Release ##
-------------

**Neptune 1.2.1**

2016 March 23

This release of Neptune adds support for Galaxy.

## Requirements ##
{'fraction_non_alphanumeric': 0.09883079638208692, 'fraction_numerical': 0.013236267372600927, 'mean_word_length': 3.4714003944773175, 'pattern_counts': {'":': 0, '<': 49, '<?xml version=': 2, '>': 49, 'https://': 2, 'lorem ipsum': 0, 'www.': 2, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1090', 'n_tokens_mistral': 1253, 'n_tokens_neox': 1127, 'n_words': 439}