Mercurial > repos > iuc > package_pathoscope_2_0_6

comparison tool_dependencies.xml @ 0:a141b2f0a911 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
author iuc
date Thu, 15 Oct 2015 13:24:55 -0400
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1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="python" version="2.7.10">
4 <repository changeset_revision="4f81728216e7" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="pathoscope" version="2.0.6">
7 <install version="1.0">
8 <actions>
9 <action type="setup_python_environment">
10 <repository changeset_revision="4f81728216e7" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
11 <package name="python" version="2.7.10" />
12 </repository>
13 <package>https://github.com/PathoScope/PathoScope/archive/v2.0.6.zip</package>
14 </action>
15 <action type="set_environment">
16 <environment_variable action="set_to" name="PYTHONPATH_PATHOSCOPE">$INSTALL_DIR</environment_variable>
17 </action>
18 </actions>
19 </install>
20 <readme>
21 Pathoscope 2.0 consists of four core and two optional analysis modules
22 for sequencing-based metagenomic profiling. The PathoLib module
23 extracts genome reference libraries (target or host/filter) from all
24 available sequences in the NCBI Nucleotide database that belong to a
25 user-defined taxonomic clade. The PathoMap module aligns the reads to
26 the target reference library and removes any reads that have sequence
27 similarity with the host or filter genomes. PathoID resolves read
28 ambiguity, identifies which of the target genomes are present in the
29 sample and estimates the proportions of reads originating from each
30 genome. PathoReport provides two report files: 1) a summary report
31 (.tsv) that contains the numbers and proportions of reads aligned to
32 each genome identified in the sample, and 2) detailed report (.xml)
33 including read coverage, read assignments, and contiguous sequences
34 generated by combining the reads. The PathoDB is an optional module
35 that provides additional annotation (organism taxonomic lineage, gene
36 loci, protein products) for all sequences identified in the sample.
37 The PathoQC module can be used to preprocess the reads prior to
38 alignment with PathoMap.
39 </readme>
40 </package>
41 </tool_dependency>