Mercurial > repos > rnateam > mirdeep2_mapper
annotate tool_dependencies.xml @ 2:f844a9c1698d draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
| author | rnateam |
|---|---|
| date | Wed, 23 Nov 2016 16:01:29 -0500 |
| parents | bda96b97c289 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="perl" version="5.18.1"> | |
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f844a9c1698d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2_mapper commit b9d202134c3c6d0e5c398c3ae75e410067fcfc52
rnateam
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1
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changeset
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4 <repository changeset_revision="95dad0955d7e" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 5 </package> |
| 6 <package name="bowtie" version="0.12.7"> | |
| 1 | 7 <repository changeset_revision="f0faa5eea2eb" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 8 </package> |
| 9 <package name="mirdeep2_mapper" version="2.0"> | |
| 10 <install version="1.0"> | |
| 11 <actions> | |
| 12 <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action> | |
| 13 <action type="move_file"> | |
| 14 <source>clip_adapters.pl</source> | |
| 15 <destination>$INSTALL_DIR</destination> | |
| 16 </action> | |
| 17 <action type="move_file"> | |
| 18 <source>collapse_reads_md.pl</source> | |
| 19 <destination>$INSTALL_DIR</destination> | |
| 20 </action> | |
| 21 <action type="move_file"> | |
| 22 <source>convert_bowtie_output.pl</source> | |
| 23 <destination>$INSTALL_DIR</destination> | |
| 24 </action> | |
| 25 <action type="move_file"> | |
| 26 <source>fastaparse.pl</source> | |
| 27 <destination>$INSTALL_DIR</destination> | |
| 28 </action> | |
| 29 <action type="move_file"> | |
| 30 <source>fastq2fasta.pl</source> | |
| 31 <destination>$INSTALL_DIR</destination> | |
| 32 </action> | |
| 33 <action type="move_file"> | |
| 34 <source>illumina_to_fasta.pl</source> | |
| 35 <destination>$INSTALL_DIR</destination> | |
| 36 </action> | |
| 37 <action type="move_file"> | |
| 38 <source>mapper.pl</source> | |
| 39 <destination>$INSTALL_DIR</destination> | |
| 40 </action> | |
| 41 <action type="move_file"> | |
| 42 <source>parse_mappings.pl</source> | |
| 43 <destination>$INSTALL_DIR</destination> | |
| 44 </action> | |
| 45 <action type="move_file"> | |
| 46 <source>rna2dna.pl</source> | |
| 47 <destination>$INSTALL_DIR</destination> | |
| 48 </action> | |
| 49 <action type="set_environment"> | |
| 50 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> | |
| 51 </action> | |
| 52 </actions> | |
| 53 </install> | |
| 54 <readme> | |
| 55 | |
| 56 Processes reads and/or maps them to the reference genome. | |
| 57 | |
| 58 input: | |
| 59 Default input is a file in fasta, seq.txt or qseq.txt format. More input can be given depending on the options used. | |
| 60 output: | |
| 61 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. | |
| 62 | |
| 63 </readme> | |
| 64 </package> | |
| 65 </tool_dependency> |