Mercurial > repos > bgruening > glimmer_not_knowledge_based
comparison glimmer_wo_icm.xml @ 0:4da5f6bdcf12 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 10:10:13 -0500 |
parents | |
children | 73c58e2debd0 |
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1 <tool id="glimmer_not_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@"> | |
2 <description>Predict ORFs in prokaryotic genomes (not knowlegde-based)</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"/> | |
7 <command><![CDATA[ | |
8 python '$__tool_directory__/glimmer_wo_icm.py' | |
9 '$input' | |
10 #if $report: | |
11 '$prediction' | |
12 #else: | |
13 'None' | |
14 #end if | |
15 #if $detailed_report: | |
16 '$detailed' | |
17 #else: | |
18 'None' | |
19 #end if | |
20 $overlap | |
21 $gene_length | |
22 $threshold | |
23 $linear | |
24 '$genes_output' | |
25 ]]></command> | |
26 <inputs> | |
27 <param name="input" type="data" format="fasta" label="Genome sequence" /> | |
28 <param name="overlap" type="integer" value="0" label="Set maximum overlap length. Overlaps this short or shorter are ignored." /> | |
29 <param name="gene_length" type="integer" value="110" label="Set minimum gene length." /> | |
30 <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene." /> | |
31 <param name="linear" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" /> | |
32 | |
33 <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file" /> | |
34 <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output" /> | |
35 </inputs> | |
36 <outputs> | |
37 <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" /> | |
38 <data name="prediction" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)"> | |
39 <filter>report == True</filter> | |
40 </data> | |
41 <data name="detailed" format="txt" label="Glimmer3 on ${on_string} (detailed report)"> | |
42 <filter>detailed_report == True</filter> | |
43 </data> | |
44 </outputs> | |
45 <tests> | |
46 <test> | |
47 <param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" /> | |
48 <param name="overlap" value="0" /> | |
49 <param name="gene_length" value="110" /> | |
50 <param name="threshold" value="30" /> | |
51 <param name="linear" value="true" /> | |
52 <param name="detailed_report" value="" /> | |
53 <param name="report" value="" /> | |
54 <output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" /> | |
55 </test> | |
56 </tests> | |
57 <help> | |
58 <![CDATA[ | |
59 | |
60 **What it does** | |
61 | |
62 This tool predicts open reading frames (ORFs) from a given DNA Sequence. That tool is not knowlegde-based. | |
63 | |
64 The recommended way is to use a trained Glimmer3 with ICM model. Use the knowlegde-based version for that and insert/generate a training set. | |
65 | |
66 ----- | |
67 | |
68 **Glimmer Overview** | |
69 | |
70 :: | |
71 | |
72 ************** ************** ************** ************** | |
73 * * * * * * * * | |
74 * long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 * | |
75 * * * * * * * * | |
76 ************** ************** ************** ************** | |
77 | |
78 ----- | |
79 | |
80 **Example** | |
81 | |
82 Suppose you have the following DNA sequences:: | |
83 | |
84 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other; | |
85 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg | |
86 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag | |
87 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc | |
88 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc | |
89 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg | |
90 ....... | |
91 | |
92 Running this tool will produce a FASTA file with predicted genes and glimmer output files like the following:: | |
93 | |
94 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other; | |
95 orf00001 577 699 +1 5.24 | |
96 orf00003 800 1123 +2 5.18 | |
97 orf00004 1144 3813 +1 10.62 | |
98 orf00006 3857 6220 +2 6.07 | |
99 orf00007 6226 7173 +1 1.69 | |
100 orf00008 7187 9307 +2 8.95 | |
101 orf00009 9424 10410 +1 8.29 | |
102 orf00010 10515 11363 +3 7.00 | |
103 orf00011 11812 11964 +1 2.80 | |
104 orf00012 12360 13457 +3 4.80 | |
105 orf00013 14379 14044 -1 7.41 | |
106 orf00015 15029 14739 -3 12.43 | |
107 orf00016 15066 15227 +3 1.91 | |
108 orf00020 16061 15351 -3 2.83 | |
109 orf00021 17513 17391 -3 2.20 | |
110 orf00023 17529 17675 +3 0.11 | |
111 | |
112 | |
113 | |
114 ]]> | |
115 </help> | |
116 <expand macro="citation" /> | |
117 </tool> |