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comparison glimmer_gbk_to_orf.xml @ 0:6351903666da draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author bgruening
date Tue, 28 Nov 2017 10:07:28 -0500
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1 <tool id="glimmer_gbk_to_orf" name="Extract ORF" version="@WRAPPER_VERSION@">
2 <description>from a GenBank file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command><![CDATA[
8 python '$__tool_directory__/glimmer_gbk_to_orf.py'
9 -g '$infile'
10 -a '$aa_output'
11 -n '$nc_output'
12 ##TODO translation table, can be extracted from genbank file directly
13 ]]></command>
14 <inputs>
15 <param name="infile" type='data' format="genbank" label="gene bank file"/>
16 </inputs>
17 <outputs>
18 <data name="aa_output" format="fasta" />
19 <data name="nc_output" format="fasta" />
20 </outputs>
21 <tests>
22 <test>
23 <param name="infile" value="test.gbk" />
24 <output name="aa_output" file="orf_aa.fa" />
25 <output name="nc_output" file="orf_nc.fa" />
26 </test>
27 </tests>
28 <help><![CDATA[
29 **What it does**
30 Read a GenBank file and export fasta formatted amino acid and CDS files.
31
32 -----
33
34 **Example**
35 * input::
36
37 Genebankfile
38
39 LOCUS BA000030 9025608 bp DNA linear BCT 21-DEC-2007
40 DEFINITION Streptomyces avermitilis MA-4680 DNA, complete genome.
41 ACCESSION BA000030 AP005021-AP005050
42 VERSION BA000030.3 GI:148878541
43 DBLINK Project: 189
44 KEYWORDS .
45 SOURCE Streptomyces avermitilis MA-4680
46 ORGANISM Streptomyces avermitilis MA-4680
47 Bacteria; Actinobacteria; Actinobacteridae; Actinomycetales;
48 Streptomycineae; Streptomycetaceae; Streptomyces.
49 REFERENCE 1
50 AUTHORS Omura,S., Ikeda,H., Ishikawa,J., Hanamoto,A., Takahashi,C.,
51 Shinose,M., Takahashi,Y., Horikawa,H., Nakazawa,H., Osonoe,T.,
52 Kikuchi,H., Shiba,T., Sakaki,Y. and Hattori,M.
53 TITLE Genome sequence of an industrial microorganism Streptomyces
54 avermitilis: deducing the ability of producing secondary
55 metabolites
56 JOURNAL Proc. Natl. Acad. Sci. U.S.A. 98 (21), 12215-12220 (2001)
57 PUBMED 11572948
58 REFERENCE 2
59 AUTHORS Ikeda,H., Ishikawa,J., Hanamoto,A., Shinose,M., Kikuchi,H.,
60 Shiba,T., Sakaki,Y., Hattori,M. and Omura,S.
61 TITLE Complete genome sequence and comparative analysis of the industrial
62 microorganism Streptomyces avermitilis
63 JOURNAL Nat. Biotechnol. 21 (5), 526-531 (2003)
64 PUBMED 12692562
65 REFERENCE 3 (bases 1 to 9025608)
66 AUTHORS Omura,S., Ikeda,H., Ishikawa,J., Hanamoto,A., Takahashi,C.,
67 Shinose,M., Takahashi,Y., Horikawa,H., Nakazawa,H., Osonoe,T.,
68 Kushida,N., Shiba,T., Sakaki,Y. and Hattori,M.
69 TITLE Direct Submission
70 JOURNAL Submitted (29-MAR-2002) Contact:S Omura Kitasato University,
71 Kitasato Institute for Life Sciences; 1-15-1 Kitasato, Sagamihara,
72 Kanagawa 228-8555, Japan URL
73 :http://avermitilis.ls.kitasato-u.ac.jp/
74 COMMENT On Jun 15, 2007 this sequence version replaced gi:57546753.
75 This work was done in collaboration with Haruo Ikeda(*1), Jun
76 Ishikawa(*2), Akiharu Hanamoto(*3), Chigusa Takahashi(*3), Mayumi
77 Shinose(*3), Hiroshi Horikawa(*4), Hidekazu Nakazawa(*4), Tomomi
78 Osonoe(*4), Norihiro Kushida(*4), Hisashi Kikuchi(*4), Tadayoshi
79 Shiba(*5), Yoshiyuki Sakaki(*6,*7), Masahira Hattori(*1,*7)
80 and Satoshi Omura(*1,*3).
81 Final finishing process and all annotation were done by H. Ikeda
82 and J. Ishikawa.
83 *1 Kitasato Institute for Life Sciences, Kitasato University *2
84 National Institute of Infectious Diseases
85 *3 The Kitasato Institute
86 *4 National Institute of Technology and Evaluation *5 School of
87 Science, Kitasato University
88 *6 Institute of Medical Science, University of Tokyo *7 RIKEN,
89 Genomic Sciences Center
90 All the annotated genes identified are available from following
91 urls.
92 http://avermitilis.ls.kitasato-u.ac.jp.
93 FEATURES Location/Qualifiers
94 source 1..9025608
95 /organism="Streptomyces avermitilis MA-4680"
96 /mol_type="genomic DNA"
97 /strain="MA-4680"
98 /db_xref="taxon:227882"
99 /note="This strain is also named as strain: ATCC 31267,
100 NCIMB 12804 or NRRL 8165."
101 gene complement(1380..1811)
102 /locus_tag="SAV_1"
103 CDS complement(1380..1811)
104 /locus_tag="SAV_1"
105 /codon_start=1
106 /transl_table=11
107 /product="hypothetical protein"
108 /protein_id="BAC67710.1"
109 /db_xref="GI:29603637"
110 /translation="MTAEWYVLVEEDTRETKRADGVELRLHRWKLAATQHIAGDQEQA
111 AAAAEDAALNYMPGVLARHARPGDEPARHAFLTQDGAWLVLLRQRHRECHIRVTTARL
112 MHTQEEKEAPPKSFKEKLRSALDGPQPPEPAGRPWKPGSET"
113
114
115 * output::
116
117 - aminoAcidOutput
118 >SAV_1
119 MTAEWYVLVEEDTRETKRADGVELRLHRWKLAATQHIAGDQEQAAAAAEDAALNYMPGVL
120 ARHARPGDEPARHAFLTQDGAWLVLLRQRHRECHIRVTTARLMHTQEEKEAPPKSFKEKL
121 RSALDGPQPPEPAGRPWKPGSET
122 >SAV_2
123 VPPQGARGTIVSATGSGKTSMAAASTLNCFPEGRILVTVPTLDLLAQTAQAWRAVGHHSP
124 MIAVCSLENDPVLNERT
125 >SAV_3
126 MDWNFPDDDIFFCGGCGDDDTPDPRVPRQDKALCVRCDRVERQVRRYRITVPRRNAIMRF
127 QRDVCALCQEGPPTDHCPDAVSFWHIDHDHRCCPPGGSCGRCVRGLLCLPCNATRLPAYE
128 RLPNVLRDSPRFNTYLNSPPARHPEARPTARDHAGPRDASSYLIDAFFTAADHPEGNALS
129 S
130 >SAV_4
131 VALTPGGTRVTQWQDRQAIGDMHERRVAAALRARGWTVQPCGQGTYPPAVREALRRTRSA
132 LRHFPDLIAARGADLITIDAKDRMPSTDTDRYAVSADTVTAGLFFTAAHAPTPLYYVFGD
133 LKVLTPAEVVHYTAHALRHRSGAFHLVRTEQAHCFDDVFGSAGAAAAA
134 >SAV_5
135 MMLLMAAYVDPRFRPTLWPGTPVPTPELMPLRGARADGEWIVWTPQVRSRSHTVPVPEDF
136 YLREFMEVDPEDLDAVAALMGAYGHLGGSINTGSWDVDVYERLKELTEREHPRAPFALHG
137 ELATLFMREAQAAITTWLALRREGGLDALIEPEVSEEELAQWQASNADLEEAWPRDLDHL
138 RELSLEIRISNLVSELNAALKPFSIGIGGLGDRYPTILAVAFLQLYNHLAEDATIRECAN
139 ETCRRHFVRQRGRAAYGQNRTSGIKYCTRECARAQAQREHRRRRKQQTTTLQQPPAPGPQ
140 SHDTSEPTAEGR
141 >SAV_6
142 MISLREHQVEANARIRAWAGFPTRSPVPAQGLRGTVVSATGSGKTITAAWAARECFRGGR
143 ILVMVPTLDLLVQTAQAWRRVGHNGPMVAACSLEKDEVLEQLGVRTTTNPIQLALWAGHG
144 PVVVFATYASLVDREDPEDVTGRAKVRGPLEAALAGGQRLYGQTMDGFDLAVVDEAHSTT
145 GDLGRPWAAIHDNSRIPADFRLYLTATPRILASPRPQKGADGRELEIATMASDPDGPYGE
146 WLFELGLSEAVERGILAGFEIDVLEIRDPSPALGESEEAQRGRRLALLQTALLEHAAARN
147 LRTVMTFHQRVEEAAAFAQTMPQTAARLYEAEVSAEALVDAGALPESSIGAEFYELEAGR
148 HVPPDRVWAAWLCGDHLVAERREVLRQFADGLDAGNKRVHRAFLASVRVLGEGVDIVGER
149 GVEAICFADTRGSQVEIVQNIGRALRPNPDGTNKTARIIVPVFLQPGENPTDMVASASFA
150 PLVTVLQGLRSHSERLVEQLASRALTSGQRHVHVKRDEDGRIIGTTTEGEGGQHESEGAV
151 ESALLHFSTPRDATTIAAFLRTRVYRPESLVWLEGYQALLRWRKKNHITGLYAVPYDTET
152 EAGVTKAFPLGRWVHQQRRTYRAGELDPHRTTLLDEAGMVWEPGDEAWENKLAALRSFHR
153 AHGHLAPRRDAVWGDADSELVPVGEHMANLRRKDGLGKNPQRAATRATQLAAIDPDWNCP
154 WPLDWQRHYRVLADLATDEPHSRLPDIQPGVQFEGDDLGKWLQRQRRSWAELSEEQQQRL
155 TALGVTPAEPPTPTPSAKGGGKAAAFQRGLAALAQWIQREGAHKVVPRGHVEAVVIDGQE
156 HQHKLGVWISNTKTRRDKLTHDQRTALAALGVEWA
157 ....
158
159 - orfs
160
161 >SAV_1
162 ATGACCGCCGAGTGGTACGTCCTCGTCGAAGAGGACACACGAGAGACCAAGCGCGCCGAC
163 GGCGTTGAACTCAGATTGCACCGCTGGAAACTGGCGGCCACTCAGCACATCGCAGGAGAT
164 CAGGAACAGGCCGCCGCCGCGGCCGAGGATGCGGCCCTGAACTACATGCCGGGAGTGCTC
165 GCTCGGCATGCCCGACCGGGAGACGAACCGGCCCGGCATGCTTTCCTCACCCAGGACGGG
166 GCCTGGCTGGTGCTCCTCAGGCAGCGGCACCGCGAGTGTCACATACGGGTGACCACTGCC
167 CGGCTCATGCATACACAGGAAGAGAAGGAGGCCCCGCCGAAAAGCTTCAAGGAGAAACTC
168 CGCAGCGCCCTGGATGGTCCTCAGCCGCCCGAACCGGCTGGTAGGCCATGGAAGCCGGGC
169 AGCGAAACCTGA
170 >SAV_2
171 GTGCCCCCTCAGGGAGCCCGTGGCACGATCGTGTCAGCTACCGGGTCCGGCAAAACGAGC
172 ATGGCCGCCGCGAGCACGCTGAACTGCTTCCCCGAAGGCCGGATCCTCGTGACCGTGCCG
173 ACCCTGGACCTGCTCGCACAGACCGCCCAGGCGTGGCGGGCAGTCGGCCACCACTCCCCC
174 ATGATCGCGGTGTGCTCGCTGGAGAACGACCCAGTGCTGAACGAGCGGACCTGA
175 >SAV_3
176 ATGGACTGGAACTTCCCCGACGACGACATCTTCTTCTGCGGCGGGTGCGGCGACGACGAC
177 ACCCCCGACCCGCGGGTCCCGCGTCAGGACAAGGCCCTGTGCGTCCGCTGCGACAGAGTC
178 GAACGGCAGGTCCGCCGATACCGGATCACCGTGCCGCGGAGGAACGCGATCATGCGCTTC
179 CAGCGCGACGTCTGCGCCCTGTGCCAGGAAGGCCCGCCGACCGACCACTGCCCCGATGCC
180 GTCAGCTTCTGGCACATCGACCACGACCACCGCTGCTGCCCTCCCGGCGGCTCATGCGGG
181 CGGTGCGTCCGCGGCCTCCTGTGCCTGCCCTGCAACGCCACCCGCCTGCCCGCCTACGAA
182 CGCCTCCCCAACGTCCTCCGCGACAGCCCTCGCTTCAACACCTACCTCAACAGCCCACCC
183 GCCCGGCACCCCGAAGCCCGCCCCACCGCCAGGGACCATGCAGGCCCCCGCGACGCATCC
184 AGCTACCTCATCGACGCCTTTTTCACCGCCGCGGACCATCCCGAGGGGAACGCCCTCAGC
185 TCCTGA
186 >SAV_4
187 GTGGCACTTACCCCAGGGGGAACCCGAGTGACGCAGTGGCAGGACCGCCAGGCGATAGGC
188 GACATGCACGAACGTCGGGTGGCGGCCGCGCTGCGCGCCCGCGGCTGGACCGTCCAGCCC
189 TGCGGACAGGGCACCTACCCGCCCGCCGTACGGGAAGCCCTGCGCCGGACCCGCTCCGCC
190 CTGCGGCACTTCCCCGACCTCATCGCCGCCCGCGGCGCCGACCTGATCACCATCGACGCC
191 AAGGACCGCATGCCCAGCACCGACACCGACCGCTACGCCGTCAGCGCCGACACCGTGACC
192 GCCGGCCTCTTTTTCACCGCGGCCCACGCTCCGACTCCGCTGTACTACGTCTTCGGCGAC
193 CTGAAGGTCCTCACGCCGGCGGAGGTGGTCCACTACACCGCTCACGCCTTGCGCCACCGC
194 AGCGGTGCCTTCCACCTCGTACGCACGGAGCAAGCACACTGCTTCGACGACGTCTTCGGA
195 TCGGCTGGCGCAGCAGCTGCGGCATGA
196 >SAV_5
197 ATGATGCTCCTCATGGCGGCATACGTTGACCCACGCTTTCGTCCTACGCTATGGCCTGGA
198 ACGCCCGTGCCGACACCGGAGTTGATGCCTCTTCGCGGAGCGCGGGCCGACGGTGAATGG
199 ATCGTCTGGACCCCGCAGGTCCGCTCCCGCTCGCACACGGTCCCCGTGCCGGAGGACTTC
200 TACCTGCGCGAGTTCATGGAGGTCGACCCTGAGGACCTCGACGCCGTGGCCGCCCTGATG
201 GGCGCCTACGGACACCTCGGCGGGAGCATCAACACCGGAAGCTGGGACGTCGACGTCTAC
202 GAGCGCCTCAAGGAGCTCACGGAGCGCGAACACCCCCGCGCGCCGTTCGCCCTGCACGGC
203 GAACTGGCCACGCTGTTCATGAGGGAGGCGCAGGCGGCCATCACCACCTGGCTGGCCCTG
204 CGCCGCGAGGGCGGGCTCGACGCGCTCATCGAGCCCGAGGTGTCCGAGGAAGAACTGGCG
205 CAGTGGCAAGCGAGCAACGCTGATCTTGAGGAAGCGTGGCCGCGGGACCTGGACCACCTG
206 CGCGAACTCTCCCTGGAGATCAGGATCAGCAACCTCGTGAGCGAACTGAACGCCGCGCTG
207 AAGCCGTTCAGCATCGGCATCGGCGGCCTGGGCGACCGCTACCCCACCATCCTCGCTGTG
208 GCGTTCCTCCAGCTCTACAACCACCTCGCCGAGGACGCCACGATCCGCGAGTGCGCGAAC
209 GAGACCTGCCGCCGCCACTTCGTACGCCAGCGCGGCCGCGCCGCATACGGGCAGAACCGC
210 ACCAGCGGCATCAAGTACTGCACCCGCGAATGCGCCCGCGCCCAGGCCCAGCGCGAACAC
211 CGCCGGCGCCGCAAACAGCAGACCACGACCCTCCAGCAGCCGCCGGCGCCTGGTCCTCAG
212 TCTCACGACACCTCAGAGCCGACTGCCGAAGGGCGCTGA
213 .......
214
215 ]]></help>
216 <expand macro="citation" />
217 </tool>