Mercurial > repos > nml > hivtrace

annotate hivtrace.xml @ 1:ba1a9be7b052 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa-dirty
author nml
date Thu, 07 Jul 2016 13:47:39 -0400
parents b81f1de20067
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
1 <?xml version="1.0"?>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
2 <tool id="hivtrace" name="HIV-Trace" version="1.0.0">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
3 <description>with options and commands</description>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
4 <requirements>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
5 <requirement type="package" version="0.1.4">hivtrace</requirement>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
6 </requirements>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
7 <stdio>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
8 <exit_code range="1:" />
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
9 </stdio>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
10 <command><![CDATA[
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
11 hivtrace
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
12
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
13 --input $inputfasta
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
14 --ambiguities $runtype.ambiguities
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
15
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
16 #if $runtype.ambiguities == "RESOLVE":
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
17 --fraction $runtype.fraction
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
18 #else
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
19 --fraction 0.05
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
20 #end if
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
21
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
22 #if $reftype.reference == "Custom":
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
23 --reference $reftype.customreference
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
24 #else
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
25 --reference $reftype.reference
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
26 #end if
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
27
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
28 --threshold $threshold
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
29
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
30 --minoverlap $minoverlap
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
31
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
32 --curate $curate
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
33
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
34 --filter $filter
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
35
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
36 #if $reftype.strip_drams:
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
37 --strip_drams $reftype.strip_drams
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
38 #end if
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
39
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
40 #if $compare:
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
41 --compare
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
42 #end if
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
43
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
44 #if $inputtype.typefasta == "aligned":
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
45 --skip-alignment
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
46 #end if
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
47
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
48 --log $logfile
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
49
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
50 > $outfile
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
51 ]]></command>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
52 <inputs>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
53 <param name="inputfasta" type="data" format="fasta" label="Sequence file"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
54
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
55 <conditional name="inputtype">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
56 <param name="typefasta" type="select" label="Type of FASTA">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
57 <option value="unaligned">Unaligned</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
58 <option value="aligned">Aligned</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
59 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
60 <when value="unaligned"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
61 <when value="aligned"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
62 </conditional>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
63
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
64 <conditional name="reftype">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
65 <param name="reference" type="select" label="Reference">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
66 <sanitizer sanitize="False" />
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
67 <option value="HXB2_prrt"> HXB2_prrt</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
68 <option value="HXB2_pol"> HXB2_pol</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
69 <option value="NL4-3_prrt"> NL4-3_prrt</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
70 <option value="HXB2_tat"> HXB2_tat</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
71 <option value="HXB2_int"> HXB2_int</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
72 <option value="HXB2_pr"> HXB2_pr</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
73 <option value="HXB2_vif"> HXB2_vif</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
74 <option value="HXB2_nef"> HXB2_nef</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
75 <option value="HXB2_vpu"> HXB2_vpu</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
76 <option value="HXB2_rev"> HXB2_rev</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
77 <option value="HXB2_vpr"> HXB2_vpr</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
78 <option value="HXB2_env"> HXB2_env</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
79 <option value="HXB2_gag"> HXB2_gag</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
80 <option value="HXB2_rt"> HXB2_rt</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
81 <option value="Custom"> Custom</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
82 <help>The sequence that will be used to align everything else to.</help>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
83 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
84 <when value="HXB2_pol">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
85 <param name="strip_drams" type="select" label="Remove DRAMS">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
86 <sanitizer sanitize="False" />
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
87 <option value="no"> No</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
88 <option value="lewis"> Mask (with ---) the list of codon sites defined in Lewis et al</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
89 <option value="wheeler"> Mask (with ---) the list of codon sites defined in Wheeler et al</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
90 <help>How to handle analyses of proteins (HIV-1 pr and/or RT only) which include drug resistance associated positions</help>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
91 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
92 </when>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
93 <when value="NL4-3_prrt"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
94 <when value="HXB2_tat"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
95 <when value="HXB2_int"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
96 <when value="HXB2_prrt">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
97 <param name="strip_drams" type="select" label="Remove DRAMS">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
98 <sanitizer sanitize="False" />
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
99 <option value="no"> No</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
100 <option value="lewis"> Mask (with ---) the list of codon sites defined in Lewis et al</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
101 <option value="wheeler"> Mask (with ---) the list of codon sites defined in Wheeler et al</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
102 <help>How to handle analyses of proteins (HIV-1 pr and/or RT only) which include drug resistance associated positions</help>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
103 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
104 </when>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
105 <when value="HXB2_pr">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
106 <param name="strip_drams" type="select" label="Remove DRAMS">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
107 <sanitizer sanitize="False" />
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
108 <option value="no"> No</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
109 <option value="lewis"> Mask (with ---) the list of codon sites defined in Lewis et al</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
110 <option value="wheeler"> Mask (with ---) the list of codon sites defined in Wheeler et al</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
111 <help>How to handle analyses of proteins (HIV-1 pr and/or RT only) which include drug resistance associated positions</help>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
112 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
113 </when>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
114 <when value="HXB2_vif"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
115 <when value="HXB2_nef"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
116 <when value="HXB2_vpu"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
117 <when value="HXB2_rev"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
118 <when value="HXB2_vpr"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
119 <when value="HXB2_env"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
120 <when value="HXB2_gag"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
121 <when value="HXB2_rt">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
122 <param name="strip_drams" type="select" label="Remove DRAMS">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
123 <sanitizer sanitize="False" />
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
124 <option value="no"> No</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
125 <option value="lewis"> Mask (with ---) the list of codon sites defined in Lewis et al</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
126 <option value="wheeler"> Mask (with ---) the list of codon sites defined in Wheeler et al</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
127 <help>How to handle analyses of proteins (HIV-1 pr and/or RT only) which include drug resistance associated positions</help>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
128 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
129 </when>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
130 <when value="Custom">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
131 <param name="customreference" type="data" format="fasta" label="Custom reference file"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
132 </when>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
133 </conditional>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
134
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
135 <param name="curate" type="select" label="Contaminant screen">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
136 <sanitizer sanitize="False" />
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
137 <option value="remove"> Remove all sequences sharing a cluster with the reference</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
138 <option value="report"> Flag all sequences sharing a cluster with the reference</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
139 <option value="no"> Do nothing</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
140 <help>What should be done if query sequences belong to the same cluster as the reference. If the reference is a database/lab strain (e.g. HXB2),
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
141 such sequences are likely mislabeled/contaminated.</help>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
142 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
143
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
144 <param name="threshold" type="float" label="Distance threshold" value="0.015"
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
145 help="Two sequences will be connected with a putative link (subject to filtering), if and only if their pairwise distance does not exceed this threshold.">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
146 <validator type="in_range" min="0" max="0.02" message="Must be between 0 and 0.02"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
147 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
148
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
149 <param name="minoverlap" type="float" label="Minimum overlap" value="500"
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
150 help="Only sequences who overlap by at least this many non-gap characters will be included in distance calculations. Be sure to adjust this based on the length of the input sequences.">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
151 <validator type="in_range" min="50" max="5000" message="Must be between 50 and 5000"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
152 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
153
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
154 <param name="filter" type="select" label="Filter edges">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
155 <sanitizer sanitize="False" />
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
156 <option value="remove"> Remove spurious edges from the inferred network</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
157 <option value="report"> Annotate spurious edges in the inferred network</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
158 <option value="no"> Do not perform filtering</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
159
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
160 <help>Use a phylogenetic test of conditional independence on each triangle in the network to remove spurious <i>transitive</i> connections which make A→B→C chains look like A-B-C triangles.</help>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
161 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
162
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
163 <conditional name="runtype">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
164 <param name="ambiguities" type="select" label="Handle Ambiguities">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
165 <sanitizer sanitize="False" />
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
166 <option value="RESOLVE"> Resolve</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
167 <option value="AVERAGE"> Average</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
168 <option value="SKIP"> Skip</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
169 <option value="GAPMM"> GAPMM</option>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
170 <help>Procedure for handling IUPAC ambiguities</help>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
171 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
172 <when value="AVERAGE"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
173 <when value="SKIP"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
174 <when value="GAPMM"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
175 <when value="RESOLVE">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
176 <param name="fraction" type="float" label="Ambiguity Fraction" value="0.05"
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
177 help="Any sequence with no more than the selected proportion [0 - 1] will have its ambiguities resolved (if possible), and ambiguities in
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
178 sequences with higher fractions of them will be averaged. This mitigates spurious linkages due to highly ambiguous sequences.">
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
179 <validator type="in_range" min="0" max="1" message="Must be between 0 and 1"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
180 </param>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
181 </when>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
182 </conditional>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
183
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
184 <param name="compare" type="boolean" truevalue="--compare" falsevalue="" checked="False" label="Compare to Los Alamos National Laboratory HIV database sequences"
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
185 help="Compare uploaded sequences to the all of the public sequences, retrieved periodically from (hiv.lanl.gov). Comparing to a public database
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
186 is only available for some of the reference sequences"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
187 </inputs>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
188 <outputs>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
189 <data name="outfile" format="txt" label="${tool.name} on ${on_string}: Results"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
190 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: Log"/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
191 </outputs>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
192
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
193 <tests>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
194 <test>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
195 <param/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
196 <output/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
197 </test>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
198 </tests>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
199
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
200 <help><![CDATA[
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
201 Options Summary for HIV-Trace
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
202
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
203 **Sequence file**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
204
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
205 A FASTA file, with nucleotide sequences to be analyzed. Each sequence will be aligned to the chosen reference sequence prior to network inference. Sequence names may include munged attributes, e.g. ISOLATE_XYZ|2005|SAN DIEGO|MSM
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
206
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
207 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
208
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
209 **Type of FASTA**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
210
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
211 Select whether your FASTA file is aligned or unaligned
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
212
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
213 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
214
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
215 **Reference**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
216
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
217 The sequence that will be used to align everything else to. It is assumed that the input sequences are in fact homologous to the reference and do not have too much indel variation
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
218
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
219 Please reference the landmarks of the HIV-1 genome if the presets seem foreign to you.
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
220
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
221 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
222
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
223 **Remove DRAMS**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
224
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
225 .. class:: infomark
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
226
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
227 **TIP:** This option is only available for four reference types: HXB2_pol, HXB2_prrt, HXB2_pr, and HXB2_rt
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
228
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
229 *Lewis* - mask (with ---) the list of codon sites defined in Lewis et al: http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0050050
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
230
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
231 *Wheeler* - mask (with ---) the list of codon sites defined in Wheeler et al: http://www.ncbi.nlm.nih.gov/pubmed/20395786
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
232
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
233 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
234
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
235 **Contaminant screen**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
236
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
237 Screen for contaminants by marking or removing sequences that cluster with any of the contaminant IDs
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
238
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
239 *Remove* - remove spurious edges from the inferred network
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
240
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
241 *Report* - flag all sequences sharing a cluster with the reference
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
242
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
243 *None* - do nothing
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
244
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
245 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
246
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
247 **Distance threshold**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
248
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
249 Two sequences will be connected with a putative link (subject to filtering, see below), if and only if their pairwise distance does not exceed this threshold
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
250
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
251 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
252
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
253 **Minimum overlap**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
254
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
255 Only sequences who overlap by at least this many non-gap characters will be included in distance calculations. Be sure to adjust this based on the length of the input sequences. You should aim to have at least 2/(distance threshold) aligned characters
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
256
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
257 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
258
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
259 **Filter edges**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
260
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
261 Use a phylogenetic test of conditional independence on each triangle in the network to remove spurious transitive connections which make A->B->C chains look like A-B-C triangles
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
262
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
263 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
264
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
265 **Handle ambiguities**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
266
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
267 Handle ambiguious nucleotides using one of the following specified strategies.
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
268
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
269 *Resolve* - count any resolutions that match as a perfect match
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
270
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
271 *Average* - average all possible resolutions
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
272
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
273 *Skip* - skip all positions with ambiguities
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
274
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
275 *GAPMM* - count character-gap positions as 4-way mismatches, otherwise same as average
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
276
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
277
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
278 For more details, please see the the MBE paper: http://mbe.oxfordjournals.org/content/22/5/1208.short
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
279
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
280 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
281
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
282 **Ambiguity fraction**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
283
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
284 .. class:: infomark
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
285
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
286 **TIP:** This option is only available when *Handle ambiguities* is set to Resolve
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
287
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
288 Affects only the Resolve option for handling ambiguities. Any sequence with no more than the selected proportion [0 - 1] will have its ambiguities resolved (if possible), and ambiguities in sequences with higher fractions of them will be averaged. This mitigates spurious linkages due to highly ambiguous sequences
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
289
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
290 -----
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
291
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
292 **Compare to Los Alamos National Laboratory HIV database sequences**
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
293
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
294 .. class:: infomark
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
295
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
296 **TIP:** This option is only available for specific reference types
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
297
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
298 Compare uploaded sequences to all public sequences. Retrieved periodically from the Los Alamos HIV Sequence Database: http://hiv.lanl.gov/
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
299 ]]></help>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
300 <citations>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
301 <citation/>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
302 </citations>
b81f1de20067 planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa
nml
parents:
diff changeset
303 </tool>