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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
author iuc
date Wed, 20 Apr 2022 16:59:05 +0000
parents ba95715078c9
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0:ba95715078c9 1:cf50aeb956f2
1 <tool id="tn93_filter" name="TN93 Filter" version="@VERSION@"> 1 <tool id="tn93_filter" name="TN93 Filter" version="@TOOL_VERSION@+galaxy1">
2 <description>- remove sequences from a reference that are within a given distance of of a cluster</description> 2 <description>- remove sequences from a reference that are within a given distance of of a cluster</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements">
7 <requirement type="package" version="@VERSION@">tn93</requirement>
8 <requirement type="package" version="1.70">biopython</requirement> 7 <requirement type="package" version="1.70">biopython</requirement>
9 </requirements> 8 </expand>
10 <version_command><![CDATA[tn93 --version]]></version_command> 9 <version_command><![CDATA[tn93 --version]]></version_command>
11 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
12 cat '$reads' > filtered_msa.fa && 11 cat '$reads' > filtered_msa.fa &&
13 tn93 -o pairwise.csv -s filtered_msa.fa -t $threshold '$clusters' && 12 tn93 -o pairwise.csv -s filtered_msa.fa -t $threshold '$clusters' &&
14 python '$__tool_directory__/tn93_filter.py' --reference '$reference' 13 python '$__tool_directory__/tn93_filter.py' --reference '$reference'
18 ]]></command> 17 ]]></command>
19 <inputs> 18 <inputs>
20 <param name="reads" type="data" format="fasta" label="Aligned reads" /> 19 <param name="reads" type="data" format="fasta" label="Aligned reads" />
21 <param name="reference" type="data" format="fasta" label="Reference sequence" /> 20 <param name="reference" type="data" format="fasta" label="Reference sequence" />
22 <param name="clusters" type="data" format="fasta" label="FASTA file with compressed clusters" /> 21 <param name="clusters" type="data" format="fasta" label="FASTA file with compressed clusters" />
23 <param name="threshold" type="float" value="0.015" label="Pairwise distance threshold" /> 22 <param name="threshold" type="float" value="0.015" min="0" max="1" label="Pairwise distance threshold" />
24 </inputs> 23 </inputs>
25 <outputs> 24 <outputs>
26 <data name="filtered_reference" format="fasta" from_work_dir="filtered_msa.fa" /> 25 <data name="filtered_reference" format="fasta" from_work_dir="filtered_msa.fa" />
27 </outputs> 26 </outputs>
28 <tests> 27 <tests>
33 <param name="threshold" value="0.35" /> 32 <param name="threshold" value="0.35" />
34 <output name="filtered_reference" file="filter-out1.fasta" ftype="fasta" /> 33 <output name="filtered_reference" file="filter-out1.fasta" ftype="fasta" />
35 </test> 34 </test>
36 </tests> 35 </tests>
37 <help><![CDATA[ 36 <help><![CDATA[
38 TN93-Filter 37 TN93
39 =========== 38 ----
40 39
41 Removes aligned sequences that are within a given distance from a reference 40 This is a simple program meant to compute pairwise distances between aligned
42 sequence using the 1993 Tamura-Nei distance calculation. 41 nucleotide sequences in sequential FASTA format using the
42 [Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541).
43
44 USAGE
45 -----
46
47 usage: tn93 [-h] [-o OUTPUT] [-t THRESHOLD] [-a AMBIGS] [-l OVERLAP][-d COUNTS_IN_NAME] [-f FORMAT] [-s SECOND_FASTA] [-b] [-c] [-q] [FASTA]
48
49 Try it from using the example file in 'data' by typing
50
51 tn93 -t 0.05 -o data/test.dst data/test.fas
52
53 Output (diagnostics written to stderr, histogram written to stdout so can be redirected)
54
55 Example:
56
57 Read 8 sequences of length 1320
58 Will perform 28 pairwise distance calculations
59 Progress: 100% ( 7 links found, inf evals/sec)
60 {
61 "Actual comparisons performed" :28,
62 "Total comparisons possible" : 28,
63 "Links found" : 7,
64 "Maximum distance" : 0.0955213,
65 "Mean distance" : 0.0644451,
66 "Histogram" : [[0.005,0],[0.01,0],[0.015,0],[0.02,0],[0.025,0],[0.03,2],[0.035,1],[0.04,0],[0.045,1],[0.05,3],[0.055,1],[0.06,2],[0.065,2],[0.07,3],[0.075,4],[0.08,3],[0.085,3],[0.09,2],[0.095,0],[0.1,1],[0.105,0],[0.11,0],[0.115,0],[0.12,0],[0.125,0],[0.13,0],[0.135,0],[0.14,0],[0.145,0],[0.15,0],[0.155,0],[0.16,0],[0.165,0],[0.17,0],[0.175,0],[0.18,0],[0.185,0],[0.19,0],[0.195,0],[0.2,0],[0.205,0],[0.21,0],[0.215,0],[0.22,0],[0.225,0],[0.23,0],[0.235,0],[0.24,0],[0.245,0],[0.25,0],[0.255,0],[0.26,0],[0.265,0],[0.27,0],[0.275,0],[0.28,0],[0.285,0],[0.29,0],[0.295,0],[0.3,0],[0.305,0],[0.31,0],[0.315,0],[0.32,0],[0.325,0],[0.33,0],[0.335,0],[0.34,0],[0.345,0],[0.35,0],[0.355,0],[0.36,0],[0.365,0],[0.37,0],[0.375,0],[0.38,0],[0.385,0],[0.39,0],[0.395,0],[0.4,0],[0.405,0],[0.41,0],[0.415,0],[0.42,0],[0.425,0],[0.43,0],[0.435,0],[0.44,0],[0.445,0],[0.45,0],[0.455,0],[0.46,0],[0.465,0],[0.47,0],[0.475,0],[0.48,0],[0.485,0],[0.49,0],[0.495,0],[0.5,0],[0.505,0],[0.51,0],[0.515,0],[0.52,0],[0.525,0],[0.53,0],[0.535,0],[0.54,0],[0.545,0],[0.55,0],[0.555,0],[0.56,0],[0.565,0],[0.57,0],[0.575,0],[0.58,0],[0.585,0],[0.59,0],[0.595,0],[0.6,0],[0.605,0],[0.61,0],[0.615,0],[0.62,0],[0.625,0],[0.63,0],[0.635,0],[0.64,0],[0.645,0],[0.65,0],[0.655,0],[0.66,0],[0.665,0],[0.67,0],[0.675,0],[0.68,0],[0.685,0],[0.69,0],[0.695,0],[0.7,0],[0.705,0],[0.71,0],[0.715,0],[0.72,0],[0.725,0],[0.73,0],[0.735,0],[0.74,0],[0.745,0],[0.75,0],[0.755,0],[0.76,0],[0.765,0],[0.77,0],[0.775,0],[0.78,0],[0.785,0],[0.79,0],[0.795,0],[0.8,0],[0.805,0],[0.81,0],[0.815,0],[0.82,0],[0.825,0],[0.83,0],[0.835,0],[0.84,0],[0.845,0],[0.85,0],[0.855,0],[0.86,0],[0.865,0],[0.87,0],[0.875,0],[0.88,0],[0.885,0],[0.89,0],[0.895,0],[0.9,0],[0.905,0],[0.91,0],[0.915,0],[0.92,0],[0.925,0],[0.93,0],[0.935,0],[0.94,0],[0.945,0],[0.95,0],[0.955,0],[0.96,0],[0.965,0],[0.97,0],[0.975,0],[0.98,0],[0.985,0],[0.99,0],[0.995,0],[1,0]]
67 }
68
69 NOTES
70 -----
71
72 All sequences must be aligned and have the same length. Only IUPAC characters are recognized (e.g. no ~). Sequence names can include copy number as in
73
74 >seqname:10
75
76 ':' can be replaced with another character using `-d`, and sequences that have no explicit copy number are assumed to be a single copy. Copy numbers
77 only affect histogram and mean calculations.
43 ]]></help> 78 ]]></help>
44 <expand macro="citations"> 79 <expand macro="citations">
45 <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation> 80 <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
46 </expand> 81 </expand>
47 </tool> 82 </tool>