Mercurial > repos > iuc > getorganelle

annotate get_annotated_regions_from_gb.xml @ 2:06bcf65179fb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
author iuc
date Thu, 23 Feb 2023 17:06:37 +0000
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children 7348b69e5109
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06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
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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">
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2 <macros>
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3 <import>macros.xml</import>
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4 </macros>
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">getorganelle</requirement>
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7 <requirement type="package" version="@BIOPYTHON_VERSION@">biopython</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #import re
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11
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12 ## create list of symbolic links to input files
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13
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14 #set file_names = []
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15 #for $input in $inputs
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
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16 #set $input_name = re.sub('[^\w\-\s]', '_', str($input.name)).replace('_gb', '.gb')
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17 ln -s '$input' '$input_name' &&
06bcf65179fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle commit b7f743ebc67b5ffabac0eddf3b20960a6444365f
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18 $file_names.append($input_name)
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19 #end for
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21 ## run python script
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23 get_annotated_regions_from_gb.py
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24 #for file in file_names:
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25 '$file'
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26 #end for
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27 -o results_directory
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28 #if str($gene_type_selector) == "CDS":
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29 -t CDS
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30 #end if
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31 #if str($gene_type_selector) == "tRNA":
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32 -t tRNA
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33 #end if
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34 #if str($gene_type_selector) == "rRNA":
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35 -t rRNA
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36 #end if
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37 --mix
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38
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39 ]]></command>
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40 <inputs>
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41 <param type="data" multiple="true" name="inputs" format="gb" label="Annotated genbank file(s)" help="Genbank files with annotated regions to extract. Multiple files can be selected." />
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42 <param name="gene_type_selector" type="select" label="Gene type">
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43 <option value="CDS" selected="true">CDS</option>
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44 <option value="tRNA">tRNA</option>
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45 <option value="rRNA">rRNA</option>
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46 </param>
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47 </inputs>
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48 <outputs>
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49 <data name="output_fasta" format="fasta" from_work_dir="results_directory/gene/gene.fasta" label='${tool.name} on ${on_string}: Annotated genes'/>
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50 </outputs>
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51 <tests>
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52 <test>
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53 <param name="inputs" value="NC_047059.gb,NC_047060.gb,NC_047400.gb"/>
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54 <param name="gene_type_selector" value="CDS"/>
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55 <assert_stdout>
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56 <has_text text="Time cost" />
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57 </assert_stdout>
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58 <output name="output_fasta">
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59 <assert_contents>
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60 <has_line line=">matK CDS - NC_047059--Styphnolobium_japonicum_voucher_Yi15212-KUN_plastid__complete_genome" />
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61 <has_line line=">matK CDS - NC_047060--Haematoxylum_brasiletto_voucher_N._Zamora6857-Costa_Rica_plastid__complete_genome" />
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62 <has_line line=">matK CDS - NC_047400--Chamaecrista_mimosoides_voucher_Yi15441-KUN_plastid__complete_genome" />
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63 </assert_contents>
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64 </output>
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65 </test>
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66 <test>
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67 <param name="inputs" value="NC_047059.gb,NC_047060.gb,NC_047400.gb"/>
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68 <param name="gene_type_selector" value="tRNA"/>
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69 <assert_stdout>
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70 <has_text text="Time cost" />
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71 </assert_stdout>
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72 <output name="output_fasta">
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73 <assert_contents>
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74 <has_line line=">trnA-UGC tRNA - NC_047059--Styphnolobium_japonicum_voucher_Yi15212-KUN_plastid__complete_genome" />
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75 <has_line line=">trnA-UGC tRNA - NC_047060--Haematoxylum_brasiletto_voucher_N._Zamora6857-Costa_Rica_plastid__complete_genome" />
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76 <has_line line=">trnA-UGC tRNA - NC_047400--Chamaecrista_mimosoides_voucher_Yi15441-KUN_plastid__complete_genome" />
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77 </assert_contents>
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78 </output>
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79 </test>
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80 <test>
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81 <param name="inputs" value="NC_047059.gb,NC_047060.gb,NC_047400.gb"/>
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82 <param name="gene_type_selector" value="rRNA"/>
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83 <assert_stdout>
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84 <has_text text="Time cost" />
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85 </assert_stdout>
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86 <output name="output_fasta">
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87 <assert_contents>
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88 <has_line line=">rrn16 rRNA - NC_047059--Styphnolobium_japonicum_voucher_Yi15212-KUN_plastid__complete_genome" />
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89 <has_line line=">rrn16 rRNA - NC_047060--Haematoxylum_brasiletto_voucher_N._Zamora6857-Costa_Rica_plastid__complete_genome" />
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90 <has_line line=">rrn16 rRNA - NC_047400--Chamaecrista_mimosoides_voucher_Yi15441-KUN_plastid__complete_genome" />
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91 </assert_contents>
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92 </output>
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93 </test>
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94 </tests>
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95 <help><![CDATA[
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96
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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.
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98 Help information from the python script is below. Only options for input genebank files and gene type are included in this tool.
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99
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100 By jinjianjun@mail.kib.ac.cn 2017
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101 Usage: get_annotated_regions_from_gb.py gb_files -o out_dir
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102
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103 Options:
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104 -h, --help show this help message and exit
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105 -o OUT_PUT Output.
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106 -t GENE_TYPES Annotation type taken as gene. Default: CDS,tRNA,rRNA
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107 --separate-copy By default, only keep one copy (see '--copy-mode' for
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108 more) if there are several regions with the same name.
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109 Exception: if there are one copy with intron(s) and
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110 another copy without intron, they would be both kept.
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111 This exception was specially made for the convenience
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112 of commonly-incorrectly-annotated rps12 gene of
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113 plastome.
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114 --copy-mode=COPY_MODE
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115 first|longest|leastN|leastN_longest (default).
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116 --separate-exon By default, combining exons.
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117 --keys=GENE_KEYS The key to the gene name: gene, label, product or
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118 other keys in the qualifiers region.Default:
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119 gene,label,product,note.
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120 --mix Mix different genes into a single fasta file. In this
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121 mode, the sequence header will be gene_name - gb_info
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122 --case-mode=CASE_TREATMENT
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123 first: Gene name case-non-sensitive. Consistent to the
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124 first appearance. lower: Gene name case-non-
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125 sensitive. All gene name set to lower case. upper:
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126 Gene name case-non-sensitive. All gene name set to
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127 Upper case. raw: Gene name case-sensitive.
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128 --ignore-format-error
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129 Skip the Error: key "*" not found in annotation. Not
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130 suggested.
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131 --translate-to-product
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132 Translate the tRNA gene name to the form of their
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133 product. Default: False
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134 --overwrite Choose to overwrite previous result.
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135
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136 ]]></help>
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137 <citations>
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138 <citation type="doi">10.1093/sysbio/syaa047</citation>
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139 </citations>
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140 </tool>