| Previous changeset 0:01ed8e112f2a (2017-04-12) |
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Commit message:
planemo upload commit 93217f9e3a1bc1afc8ce971176e4ae0169a8f265 |
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README.rst regtools_junctions_extract.xml tool_dependencies.xml |
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LICENSE |
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| diff -r 01ed8e112f2a -r 06d9062f5430 LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Wed Nov 28 14:20:39 2018 -0500 |
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| b'@@ -0,0 +1,170 @@\n+Academic Free License (\xe2\x80\x9cAFL\xe2\x80\x9d) v. 3.0\n+\n+This Academic Free License (the "License") applies to any original work of\n+authorship (the "Original Work") whose owner (the "Licensor") has placed the\n+following licensing notice adjacent to the copyright notice for the Original\n+Work:\n+\n+ Licensed under the Academic Free License version 3.0\n+\n+1) Grant of Copyright License. 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| diff -r 01ed8e112f2a -r 06d9062f5430 README.rst --- a/README.rst Wed Apr 12 17:44:58 2017 -0400 +++ b/README.rst Wed Nov 28 14:20:39 2018 -0500 |
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| @@ -3,7 +3,7 @@ This is a modified Galaxy wrapper for regtools which is based on the previous wrapper written by Remi Marenco (https://github.com/remimarenco/regtools). "regtools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context" (https://regtools.readthedocs.io/en/latest/). -This wrapper adds an validation step to check if the output files are valid BED format. The lines with invalid strand (neighter "+" or "-") will be removed. +This wrapper adds an validation step to check if the output files are valid BED format. The lines with invalid strand (neither "+" or "-") will be removed. This wrapper creates a new 13th column to store the scores. The scores in column 4 will be changed to 1000. |
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| diff -r 01ed8e112f2a -r 06d9062f5430 regtools_junctions_extract.xml --- a/regtools_junctions_extract.xml Wed Apr 12 17:44:58 2017 -0400 +++ b/regtools_junctions_extract.xml Wed Nov 28 14:20:39 2018 -0500 |
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| @@ -1,7 +1,7 @@ -<tool id="regtools_junctions_extract" name="regtools junctions extract" version="0.1.0"> +<tool id="regtools_junctions_extract" name="regtools junctions extract" version="0.1.1"> <description>Extract splice junctions from a RNA-Seq BAM file</description> <requirements> - <requirement type="package" version="0.3.0">regtools</requirement> + <requirement type="package" version="0.5.0">regtools</requirement> </requirements> <stdio> <exit_code range="1:" /> |
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| diff -r 01ed8e112f2a -r 06d9062f5430 tool_dependencies.xml --- a/tool_dependencies.xml Wed Apr 12 17:44:58 2017 -0400 +++ b/tool_dependencies.xml Wed Nov 28 14:20:39 2018 -0500 |
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| @@ -1,19 +1,17 @@ -<?xml version="1.0"?> +<?xml version="1.0" ?> <tool_dependency> - <package name="regtools" version="0.3.0"> + <package name="regtools" version="0.5.0"> <install version="1.0"> <actions> - <action type="shell_command">git clone --recursive https://github.com/griffithlab/regtools.git</action> + <action type="shell_command">git clone http://github.com/griffithlab/regtools --recursive -b 0.5.0</action> <action type="make_directory">build</action> <action type="change_directory">build</action> - <action type="set_environment_for_install"> <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="cmake" version="3.2.3" /> + <package name="cmake" version="3.2.3"/> </repository> </action> <action type="shell_command">cmake ..</action> - <action type="shell_command">make</action> <action type="move_file"> <source>regtools</source> @@ -25,4 +23,4 @@ </actions> </install> </package> -</tool_dependency> +</tool_dependency> \ No newline at end of file |