Mercurial > repos > iuc > getorganelle

annotate get_annotated_regions_from_gb.xml @ 5:ba88bc5a6446 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit 5a871a3fb322bf6d69ff0198111d3ce53b802d94
author iuc
date Mon, 15 Apr 2024 06:27:37 +0000
parents 7348b69e5109
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
1 <tool id="get_annotated_regions_from_gb" name="Get annotated regions from genbank files (getorganelle)" version="0.1.0" python_template_version="3.5">
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
2 <macros>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
3 <import>macros.xml</import>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
4 </macros>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
5 <requirements>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">getorganelle</requirement>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
7 <requirement type="package" version="@BIOPYTHON_VERSION@">biopython</requirement>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
8 </requirements>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
10 #import re
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
11
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
12 ## create list of symbolic links to input files
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
13
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
14 #set file_names = []
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
15 #for $input in $inputs
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
16 #set $input_name = re.sub('[^\w\-\s]', '_', str($input.name)).replace('_gb', '.gb')
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
17 ln -s '$input' '$input_name' &&
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
18 $file_names.append($input_name)
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
19 #end for
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
20
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
21 ## run python script
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
22
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
23 get_annotated_regions_from_gb.py
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
24 #for file in file_names:
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
25 '$file'
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
26 #end for
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
27 -o results_directory
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
28 #if str($gene_type_selector) == "CDS":
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
29 -t CDS
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
30 #end if
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
31 #if str($gene_type_selector) == "tRNA":
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
32 -t tRNA
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
33 #end if
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
34 #if str($gene_type_selector) == "rRNA":
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
35 -t rRNA
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
36 #end if
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
37 --mix
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
38
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
39 ]]></command>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
40 <inputs>
4
7348b69e5109 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b6e175a6e2ed3b9dfb753aa61cb55c8bc5b44bfd
iuc
parents: 2
diff changeset
41 <param type="data" multiple="true" name="inputs" format="genbank" label="Annotated genbank file(s)" help="Genbank files with annotated regions to extract. Multiple files can be selected." />
2
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
42 <param name="gene_type_selector" type="select" label="Gene type">
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
43 <option value="CDS" selected="true">CDS</option>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
44 <option value="tRNA">tRNA</option>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
45 <option value="rRNA">rRNA</option>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
46 </param>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
47 </inputs>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
48 <outputs>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
49 <data name="output_fasta" format="fasta" from_work_dir="results_directory/gene/gene.fasta" label='${tool.name} on ${on_string}: Annotated genes'/>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
50 </outputs>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
51 <tests>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
52 <test>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
53 <param name="inputs" value="NC_047059.gb,NC_047060.gb,NC_047400.gb"/>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
54 <param name="gene_type_selector" value="CDS"/>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
55 <assert_stdout>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
56 <has_text text="Time cost" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
57 </assert_stdout>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
58 <output name="output_fasta">
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
59 <assert_contents>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
60 <has_line line=">matK CDS - NC_047059--Styphnolobium_japonicum_voucher_Yi15212-KUN_plastid__complete_genome" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
61 <has_line line=">matK CDS - NC_047060--Haematoxylum_brasiletto_voucher_N._Zamora6857-Costa_Rica_plastid__complete_genome" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
62 <has_line line=">matK CDS - NC_047400--Chamaecrista_mimosoides_voucher_Yi15441-KUN_plastid__complete_genome" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
63 </assert_contents>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
64 </output>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
65 </test>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
66 <test>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
67 <param name="inputs" value="NC_047059.gb,NC_047060.gb,NC_047400.gb"/>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
68 <param name="gene_type_selector" value="tRNA"/>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
69 <assert_stdout>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
70 <has_text text="Time cost" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
71 </assert_stdout>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
72 <output name="output_fasta">
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
73 <assert_contents>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
74 <has_line line=">trnA-UGC tRNA - NC_047059--Styphnolobium_japonicum_voucher_Yi15212-KUN_plastid__complete_genome" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
75 <has_line line=">trnA-UGC tRNA - NC_047060--Haematoxylum_brasiletto_voucher_N._Zamora6857-Costa_Rica_plastid__complete_genome" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
76 <has_line line=">trnA-UGC tRNA - NC_047400--Chamaecrista_mimosoides_voucher_Yi15441-KUN_plastid__complete_genome" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
77 </assert_contents>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
78 </output>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
79 </test>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
80 <test>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
81 <param name="inputs" value="NC_047059.gb,NC_047060.gb,NC_047400.gb"/>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
82 <param name="gene_type_selector" value="rRNA"/>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
83 <assert_stdout>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
84 <has_text text="Time cost" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
85 </assert_stdout>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
86 <output name="output_fasta">
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
87 <assert_contents>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
88 <has_line line=">rrn16 rRNA - NC_047059--Styphnolobium_japonicum_voucher_Yi15212-KUN_plastid__complete_genome" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
89 <has_line line=">rrn16 rRNA - NC_047060--Haematoxylum_brasiletto_voucher_N._Zamora6857-Costa_Rica_plastid__complete_genome" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
90 <has_line line=">rrn16 rRNA - NC_047400--Chamaecrista_mimosoides_voucher_Yi15441-KUN_plastid__complete_genome" />
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
91 </assert_contents>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
92 </output>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
93 </test>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
94 </tests>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
95 <help><![CDATA[
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
96
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
97 Python script to extract annotated genes from genbank files. The annotated genes are in the correct format to be used as seed sequences in GetOrganelle.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
98 Help information from the python script is below. Only options for input genebank files and gene type are included in this tool.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
99
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
100 By jinjianjun@mail.kib.ac.cn 2017
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
101 Usage: get_annotated_regions_from_gb.py gb_files -o out_dir
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
102
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
103 Options:
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
104 -h, --help show this help message and exit
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
105 -o OUT_PUT Output.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
106 -t GENE_TYPES Annotation type taken as gene. Default: CDS,tRNA,rRNA
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
107 --separate-copy By default, only keep one copy (see '--copy-mode' for
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
108 more) if there are several regions with the same name.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
109 Exception: if there are one copy with intron(s) and
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
110 another copy without intron, they would be both kept.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
111 This exception was specially made for the convenience
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
112 of commonly-incorrectly-annotated rps12 gene of
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
113 plastome.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
114 --copy-mode=COPY_MODE
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
115 first|longest|leastN|leastN_longest (default).
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
116 --separate-exon By default, combining exons.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
117 --keys=GENE_KEYS The key to the gene name: gene, label, product or
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
118 other keys in the qualifiers region.Default:
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
119 gene,label,product,note.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
120 --mix Mix different genes into a single fasta file. In this
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
121 mode, the sequence header will be gene_name - gb_info
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
122 --case-mode=CASE_TREATMENT
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
123 first: Gene name case-non-sensitive. Consistent to the
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
124 first appearance. lower: Gene name case-non-
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
125 sensitive. All gene name set to lower case. upper:
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
126 Gene name case-non-sensitive. All gene name set to
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
127 Upper case. raw: Gene name case-sensitive.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
128 --ignore-format-error
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
129 Skip the Error: key "*" not found in annotation. Not
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
130 suggested.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
131 --translate-to-product
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
132 Translate the tRNA gene name to the form of their
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
133 product. Default: False
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
134 --overwrite Choose to overwrite previous result.
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
135
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
136 ]]></help>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
137 <citations>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
138 <citation type="doi">10.1093/sysbio/syaa047</citation>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
139 </citations>
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
iuc
parents:
diff changeset
140 </tool>