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comparison tool_dependencies.xml @ 0:80c9599143f7 draft

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author rnateam
date Fri, 16 Jan 2015 08:43:27 -0500
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="perl" version="5.18.1">
4 <repository changeset_revision="a1a111b9faa5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="bowtie" version="0.12.7">
7 <repository changeset_revision="f54826948b0b" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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>