Mercurial > repos > bgruening > glimmer_build_icm
comparison glimmer_build_icm.xml @ 0:9c195b26a5ac draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author | bgruening |
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date | Tue, 28 Nov 2017 10:08:06 -0500 |
parents | |
children | cc51783dc93c |
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1 <tool id="glimmer_build_icm" name="Glimmer ICM builder" version="@WRAPPER_VERSION@"> | |
2 <description></description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command><![CDATA[ | |
8 build-icm | |
9 --depth $depth | |
10 $no_stops | |
11 --period $period | |
12 --width $width | |
13 | |
14 #if $stop_codon_opts.stop_codon_opts_selector == "gb": | |
15 --trans_table '${stop_codon_opts.genbank_gencode}' | |
16 #else: | |
17 --stop_codons '${stop_codon_opts.stop_codons}' | |
18 #end if | |
19 | |
20 '$outfile' < '$infile' 2>&1; | |
21 ]]></command> | |
22 <inputs> | |
23 <param name="infile" type="data" format="fasta" label="Trainings Dataset" help="A set of known genes in FASTA format." /> | |
24 <param name="depth" type="integer" value="7" label="Set the depth of the ICM" help="The depth is the maximum number of positions in the context window that will be used to determine the probability of the predicted position." /> | |
25 <param name="period" type="integer" value="3" label="Set the period of the ICM" help="The period is the number of different submodels for different positions in the text in a cyclic pattern. E.g., if the period is 3, the first submodel will determine positions 1, 4, 7, ..." /> | |
26 <param name="width" type="integer" value="12" label="Set the width of the ICM" help="The width includes the predicted position." /> | |
27 <param name="no_stops" type="boolean" truevalue="--no_stops" falsevalue="" checked="false" label="Do not use any input strings with in-frame stop codons" /> | |
28 | |
29 <conditional name="stop_codon_opts"> | |
30 <param name="stop_codon_opts_selector" type="select" label="Specify start codons as"> | |
31 <option value="gb" selected="True">Genbank translation table entry</option> | |
32 <option value="free_form">Comma-separated list</option> | |
33 </param> | |
34 <when value="gb"> | |
35 <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons"> | |
36 <option value="1" selected="True">1. Standard</option> | |
37 <option value="2">2. Vertebrate Mitochondrial</option> | |
38 <option value="3">3. Yeast Mitochondrial</option> | |
39 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
40 <option value="5">5. Invertebrate Mitochondrial</option> | |
41 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
42 <option value="9">9. Echinoderm Mitochondrial</option> | |
43 <option value="10">10. Euplotid Nuclear</option> | |
44 <option value="11">11. Bacteria and Archaea</option> | |
45 <option value="12">12. Alternative Yeast Nuclear</option> | |
46 <option value="13">13. Ascidian Mitochondrial</option> | |
47 <option value="14">14. Flatworm Mitochondrial</option> | |
48 <option value="15">15. Blepharisma Macronuclear</option> | |
49 <option value="16">16. Chlorophycean Mitochondrial</option> | |
50 <option value="21">21. Trematode Mitochondrial</option> | |
51 <option value="22">22. Scenedesmus obliquus mitochondrial</option> | |
52 <option value="23">23. Thraustochytrium Mitochondrial</option> | |
53 <option value="24">24. Pterobranchia mitochondrial</option> | |
54 </param> | |
55 </when> | |
56 <when value="free_form"> | |
57 <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" /> | |
58 </when> | |
59 </conditional> | |
60 </inputs> | |
61 <outputs> | |
62 <data format="data" name="outfile" /> | |
63 </outputs> | |
64 <tests> | |
65 <test> | |
66 <param name="infile" value='streptomyces_Tu6071_plasmid_genes.fasta' /> | |
67 <param name="depth" value="7" /> | |
68 <param name="period" value="3" /> | |
69 <param name="width" value="12" /> | |
70 <param name="no_stops" value="" /> | |
71 <param name="genbank_gencode" value="11" /> | |
72 <!-- compare files sizes, because the output is a binary --> | |
73 <output name="outfile" file='streptomyces_Tu6071_plasmid_genes.icm' compare="sim_size" delta="1000" ftype="data" /> | |
74 </test> | |
75 </tests> | |
76 | |
77 <help> | |
78 <![CDATA[ | |
79 | |
80 **What it does** | |
81 | |
82 This program constructs an interpolated context model (ICM) from an input set of sequences. | |
83 | |
84 This model can be used by Glimmer3 to predict genes. | |
85 | |
86 **TIP** To extract CDS from a GenBank file use the tool *Extract ORF from a GenBank file*. | |
87 | |
88 ----- | |
89 | |
90 **Example** | |
91 | |
92 *Input*:: | |
93 | |
94 - Genome Sequence | |
95 | |
96 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7 | |
97 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT | |
98 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT | |
99 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT | |
100 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC | |
101 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA | |
102 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG | |
103 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA | |
104 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA | |
105 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC | |
106 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA | |
107 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC | |
108 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC | |
109 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA | |
110 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC | |
111 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT | |
112 ..... | |
113 | |
114 *Output*:: | |
115 interpolated context model (ICM) | |
116 | |
117 | |
118 | |
119 ]]> | |
120 </help> | |
121 <expand macro="citation" /> | |
122 </tool> |