Mercurial > repos > iuc > package_pathoscope_2_0_6

annotate tool_dependencies.xml @ 1:ccf97ee7a024 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
author iuc
date Tue, 22 Dec 2015 19:26:46 -0500
parents a141b2f0a911
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
2 <tool_dependency>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
3 <package name="python" version="2.7.10">
1
ccf97ee7a024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
parents: 0
diff changeset
4 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
5 </package>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
6 <package name="pathoscope" version="2.0.6">
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
7 <install version="1.0">
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
8 <actions>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
9 <action type="setup_python_environment">
1
ccf97ee7a024 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
parents: 0
diff changeset
10 <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
11 <package name="python" version="2.7.10" />
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
12 </repository>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
13 <package>https://github.com/PathoScope/PathoScope/archive/v2.0.6.zip</package>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
14 </action>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
15 <action type="set_environment">
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
16 <environment_variable action="set_to" name="PYTHONPATH_PATHOSCOPE">$INSTALL_DIR</environment_variable>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
17 </action>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
18 </actions>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
19 </install>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
20 <readme>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
21 Pathoscope 2.0 consists of four core and two optional analysis modules
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
22 for sequencing-based metagenomic profiling. The PathoLib module
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
23 extracts genome reference libraries (target or host/filter) from all
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
24 available sequences in the NCBI Nucleotide database that belong to a
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
25 user-defined taxonomic clade. The PathoMap module aligns the reads to
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
26 the target reference library and removes any reads that have sequence
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
27 similarity with the host or filter genomes. PathoID resolves read
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
28 ambiguity, identifies which of the target genomes are present in the
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
29 sample and estimates the proportions of reads originating from each
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
30 genome. PathoReport provides two report files: 1) a summary report
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
31 (.tsv) that contains the numbers and proportions of reads aligned to
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
32 each genome identified in the sample, and 2) detailed report (.xml)
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
33 including read coverage, read assignments, and contiguous sequences
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
34 generated by combining the reads. The PathoDB is an optional module
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
35 that provides additional annotation (organism taxonomic lineage, gene
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
36 loci, protein products) for all sequences identified in the sample.
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
37 The PathoQC module can be used to preprocess the reads prior to
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
38 alignment with PathoMap.
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
39 </readme>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
40 </package>
a141b2f0a911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_pathoscope_2_0_6 commit 3c29d3c8710ca23b4c59c2cf8501697331a65ac0-dirty
iuc
parents:
diff changeset
41 </tool_dependency>