Mercurial > repos > rnateam > mirdeep2_mapper

diff tool_dependencies.xml @ 3:79fdac89dd6e draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit 04c75332ac618b43ce5c3f307f7866e97147e865
author rnateam
date Thu, 05 Apr 2018 08:54:49 -0400
parents f844a9c1698d
children
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--- a/tool_dependencies.xml	Wed Nov 23 16:01:29 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bowtie" version="0.12.7">
-        <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="mirdeep2_mapper" version="2.0">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action>
-                <action type="move_file">
-                    <source>clip_adapters.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>collapse_reads_md.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>convert_bowtie_output.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>fastaparse.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>fastq2fasta.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>illumina_to_fasta.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>mapper.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>parse_mappings.pl</source>
-                    <destination>$INSTALL_DIR</destination>
-                </action>
-                <action type="move_file">
-                    <source>rna2dna.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>
-
-Processes reads and/or maps them to the reference genome.
-
-input:
-Default input is a file in fasta, seq.txt or qseq.txt format. More input can be given depending on the options used.
-output:
-The output depends on the options used (see below). Either a fasta file with processed reads or an arf file with with mapped reads, or both, are output. 
-
-        </readme>
-    </package>
-</tool_dependency>