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

--- 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>