Mercurial > repos > rnateam > mirdeep2_quantifier
diff tool_dependencies.xml @ 2:d5ea61ff12eb draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_quantifier commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
author | rnateam |
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date | Wed, 12 Jul 2017 14:41:05 -0400 |
parents | 40dc77f3730c |
children |
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--- a/tool_dependencies.xml Wed Feb 04 12:45:52 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,45 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="perl" version="5.18.1"> - <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bowtie" version="0.12.7"> - <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="vienna_rna" version="1.8.5"> - <repository changeset_revision="6757330f89cd" name="package_vienna_rna_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="pdf_api2" version="2.023"> - <repository changeset_revision="b9b7fadfdb69" name="package_perl_pdf_api2_2_023" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="mirdeep2_quantifier" version="2.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-quantifier.tar.gz</action> - <action type="move_file"> - <source>quantifier.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>make_html2.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="move_file"> - <source>convert_bowtie_output.pl</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - <readme> - -The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs. -First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too. -By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors. -The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined. - - </readme> - </package> -</tool_dependency>