Mercurial > repos > artbio > fetch_fasta_from_ncbi

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi commit 1a90ac7cdeb35399011207ab43c78043fd5c7287
author artbio
date Sat, 14 Oct 2023 22:34:56 +0000
parents 706fe8139955
children
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6
4af77e1af12a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi commit 1a90ac7cdeb35399011207ab43c78043fd5c7287
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1 <tool id="retrieve_fasta_from_NCBI" name="Retrieve FASTA from NCBI" version="3.1.0">
5
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.25.9">urllib3</requirement>
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5 </requirements>
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6 <command><![CDATA[
4
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7 python '$__tool_directory__'/fetch_fasta_from_NCBI.py
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8 #if $query.option == 'query':
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9 --query '$query.queryString'
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10 #else:
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11 --iud_file '$query.iud_list'
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12 #end if
706fe8139955 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b5ef783237b244d684e26b1ed1cc333a8305ce3e"
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13 --dbname '$dbname'
706fe8139955 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b5ef783237b244d684e26b1ed1cc333a8305ce3e"
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14 --logfile '$logfile'
706fe8139955 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/fetch_fasta_from_ncbi commit b5ef783237b244d684e26b1ed1cc333a8305ce3e"
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15 #if $fetch_option == 'fasta':
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16 --fasta $fasta
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17 #end if
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18 ]]></command>
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19 <inputs>
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20
5
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21 <conditional name="query">
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22 <param name="option" type="select" label="retrieve data from query or IUD list" display="radio">
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23 <option value="query" selected="true">Query string</option>
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24 <option value="list">IUD list</option>
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25 </param>
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26 <when value="query">
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27 <param name="queryString" type="text" size="5x80" area="True"
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28 value=""
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29 label="Query to NCBI in entrez format"
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30 help="exemple: `Drosophila melanogaster[Organism] AND Gcn5[Title]`">
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31 <sanitizer>
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32 <valid initial="string.printable">
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33 <remove value="&quot;"/>
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34 <remove value="\"/>
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35 </valid>
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36 <mapping initial="none">
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37 <add source="&quot;" target="\&quot;"/>
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38 <add source="\" target="\\"/>
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39 </mapping>
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40 </sanitizer>
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41 </param>
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42 </when>
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43 <when value="list">
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44 <param name="iud_list" format="txt,tabular" type="data" label="A list of NCBI UIDs"
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45 help="a file with a single column of UIDs, in txt or tabular format"/>
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46 </when>
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47 </conditional>
1
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48 <param name="dbname" type="select" label="NCBI database">
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49 <option value="nuccore">Nucleotide</option>
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50 <option value="protein">Protein</option>
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51 </param>
5
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52 <param name="fetch_option" type="select" label="select what will be retrieved">
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53 <option value="fasta" selected="true">Fasta and IUDs</option>
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54 <option value="justiuds">Only IUDs</option>
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55 </param>
1
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56 </inputs>
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57 <outputs>
5
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58 <data name="fasta" format="fasta" label="Fasta sequences retrieved from NCBI" >
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59 <filter>fetch_option == "fasta"</filter>
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60 </data>
5
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61 <data name="UIDs" format="txt" label="UIDs" from_work_dir="retrieved_uid_list.txt">
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62 <filter>query['option'] == "query"</filter>
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63 </data>
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64 <data format="txt" name="logfile" label="logs"/>
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65 </outputs>
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66 <tests>
6
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67 <test expect_num_outputs="3">
4
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68 <param name="queryString" value="9629650[gi]" />
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69 <param name="dbname" value="nuccore" />
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70 <param name="fetch_option" value="fasta"/>
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71 <output name="fasta" ftype="fasta" file="output.fa" />
4
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72 </test>
6
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73 <test expect_num_outputs="2">
4
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74 <param name="queryString" value="CU929326[Accession]" />
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75 <param name="dbname" value="nuccore" />
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76 <param name="fetch_option" value="justiuds"/>
4
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77 <output name="logfile" ftype="txt" file="dry_run.log" compare="sim_size"/>
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78 </test>
6
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79 <test expect_num_outputs="2">
5
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80 <param name="option" value="list" />
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81 <param name="iud_list" value="input_list.txt" ftype="txt" />
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82 <param name="dbname" value="nuccore" />
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83 <param name="fetch_option" value="fasta"/>
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84 <output name="fasta" ftype="fasta" file="output_list.fa"/>
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85 </test>
6
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86 <test expect_num_outputs="3">
5
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87 <param name="queryString" value="Drosophila[Organism] AND 2017[Modification Date] AND virus" />
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88 <param name="dbname" value="nuccore" />
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89 <param name="fetch_option" value="fasta"/>
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90 <output name="fasta" ftype="fasta" >
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91 <metadata name="sequences" value="2" />
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92 </output>
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93 </test>
6
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94 <test expect_num_outputs="2">
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95 <param name="queryString" value="labalbalbalbaalablalbabal[Title]" />
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96 <param name="dbname" value="nuccore" />
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97 <param name="fetch_option" value="justiuds"/>
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98 <output name="logfile" ftype="txt">
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99 <assert_contents>
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100 <has_line_matching expression=".*Found\s+0\s+UIDs" />
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101 </assert_contents>
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102 </output>
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103 </test>
1
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104 </tests>
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105 <help>
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106 **What it does**
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107
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108 This tool retrieves nucleotide/peptide sequences from the corresponding
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109 NCBI database (nuccore or protein) for a given entrez query.
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110
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111 The tool can be set with the query
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112 "txid10239[orgn] NOT txid131567[orgn] AND complete NOT partial[title] NOT phage[title]"
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113 for metaVisitor use purpose
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114
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115 See `Entrez help`_ for explanation of query formats
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116
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117 Be sure to use the appropriate NCBI query syntax. Always use [] to specify the search fields.
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118
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119 By checking the checkbox you can also run your query without sequence
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120 retrieval and get the number of sequences your query will fetch.
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121
1
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122 Note that the tool may fail in case of interrupted connexion with the NCBI database (see the log dataset)
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123
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124 Retrieval progress is reported in the log dataset.
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125
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126 **Options**::
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127 <![CDATA[
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128 usage: fetch_fasta_from_NCBI.py [-h] [--query QUERY_STRING]
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129 [--iud_file IUDS_FILE] [--output OUTNAME]
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130 [--dbname DBNAME] [--fasta GET_FASTA]
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131 [--logfile LOGFILE]
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132 [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
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133
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134 Retrieve data from NCBI
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135
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136 optional arguments:
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137 -h, --help show this help message and exit
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138 --query QUERY_STRING, -i QUERY_STRING
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139 NCBI Query String
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140 --iud_file IUDS_FILE input list of iuds to be fetched
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141 --output OUTNAME, -o OUTNAME
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142 output file name
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143 --dbname DBNAME, -d DBNAME
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144 database type
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145 --fasta GET_FASTA, -F GET_FASTA
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146 retrieve fasta sequences
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147 --logfile LOGFILE, -l LOGFILE
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148 log file (default=stderr)
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149 --loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL}
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150 logging level (default: INFO)
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151 ]]>
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152
1
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153
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154 .. _Entrez help: https://www.ncbi.nlm.nih.gov/books/NBK3837/#EntrezHelp.Entrez_Searching_Options
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155
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156 </help>
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157 <citations>
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158 <citation type="doi">10.1186/1471-2105-14-73</citation>
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159 </citations>
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160 </tool>