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author dcouvin
date Wed, 15 Sep 2021 21:35:09 +0000
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1 <tool id="getseqinfo" name="getSequenceInfo tool" version="1.0.1">
2 <description>allows to extract sequence data and specific information from GenBank </description>
3
4 <requirements>
5 <requirement type="package" version="1.7.2">perl-bioperl</requirement>
6 <requirement type="package" version="2.32">perl-archive-tar</requirement>
7 <requirement type="package" version="0.45">perl-file-copy-recursive</requirement>
8 <requirement type="package" version="2.16">perl-file-path</requirement>
9 <requirement type="package" version="2.79">perl-net-ftp</requirement>
10 <requirement type="package" version="2.064">perl-io-uncompress-gunzip</requirement>
11 <requirement type="package" version="6.15">perl-lwp-simple</requirement>
12 <requirement type="package" version="1.38_03">perl-posix</requirement>
13 </requirements>
14
15 <!--<command interpreter="bash">
16 ./getSequenceInfo.sh genbank $availableKingdom $assemblylevel $species $quantity $output1
17 perl $directory/getSequenceInfo.pl -directory $dir -k $availableKingdoms -l $assemblylevel -s $species -n $quantity -o $output
18
19 mv results/folder/result/summary.html $summary_html &&
20 mv results/folder/result/summary.xls $summary_tsv &&
21
22 (mv results/folder/result/Assemby/*.fna ./assembly/ 2> /dev/null || true) &&
23
24 (mv results/folder/result/GenBank/*.gbk ./genbanks/ 2> /dev/null || true)
25
26 var1="genbank_";var2=$availableKingdoms_assembly_summary.txt"
27
28 if [ -f "./results/result/${keyword}_folder/${keyword}.fasta" ]; then
29 mv ./results/result/${keyword}_folder/${keyword}.fasta ./assembly/${keyword}.fna;
30 fi
31
32
33 </command>-->
34
35 <command detect_errors="aggressive"><![CDATA[
36 perl $__tool_directory__/getSequenceInfo.pl -k "$availableKingdoms"
37 #if $search == "1"
38 -taxid "$species"
39 #else if $search == "0"
40 -s "$species"
41 #end if
42 -level "$assemblyLevel"
43 #if $component == "" and $keyword != ''
44 -c "$keyword"
45 #else if $component != "" and $keyword == ""
46 -c "$component"
47 #else if $component != "" and $keyword != ""
48 -c "${component},${keyword}"
49 #end if
50 -n $quantity -date "$date"
51 -path "${__tool_directory__}/genbank_${availableKingdoms}_assembly_summary.txt" -o ./results &&
52 mkdir ./assembly/ &&
53 mkdir ./genbanks/ &&
54 mkdir ./reports/ &&
55 mv ./results/result/summary.xls $summary_tsv &&
56 mv ./results/result/GenBank/*.gbff ./genbanks/ &&
57 mv ./results/result/Assembly/*.fna ./assembly/ &&
58 mv ./results/result/Report/*.txt ./reports/ &&
59 if [ -f "./results/result/${component}_folder/${component}.fasta" ]; then
60 mv ./results/result/${component}_folder/${component}.fasta ./assembly/${component}.fna;
61 fi &&
62 if [ -f "./results/result/${keyword}_folder/${keyword}.fasta" ]; then
63 mv ./results/result/${keyword}_folder/${keyword}.fasta ./assembly/${keyword}.fna;
64 fi
65 && rm -r ./results/
66
67 ]]></command>
68
69
70 <inputs>
71
72 <param name="availableKingdoms" type="select" label="Select the kingdom:">
73 <option value="bacteria">bacteria</option>
74 <option value="protozoa">protozoa</option>
75 <option value="viral">viral</option>
76 </param>
77
78 <param name="search" type="select" display="radio" label="Choose between Species (organism's name) or NCBI Taxonomy ID (TaxID)">
79 <option value="0">Species</option>
80 <option value="1">TaxID</option>
81 </param>
82 <param name="species" type="text" area="false" label="Species or NCBI TaxID (eg. Escherichia coli):"/>
83
84 <param name="assemblyLevel" type="select" label="Assembly level:">
85 <option value="Complete Genome">Complete Genome</option>
86 <option value="Complete Genome,Chromosome,Scaffold,Contig">All</option>
87 </param>
88
89 <param name="component" type="select" label="Sequence component:">
90 <option value=""></option>
91 <option value="plasmid">Plasmid</option>
92 <option value="chromosome">Chromosome</option>
93 <!--<option value="keyword"><param name="keyword" type="text" area="false" label="OR use a keyword:"/></option>-->
94 </param>
95 <param name="keyword" type="text" area="false" label="OR use a keyword (sequences having a description containing this keyword will be dowloaded in a separate file):"/>
96
97 <param name="quantity" type="text" area="false" value="3" label="Number of assemblies:"/>
98 <param name="date" type="text" value="0000-00-00" area="false" label="From Release date (yyyy-mm-dd):"/>
99
100
101 </inputs>
102
103 <outputs>
104 <collection name="output" type="list" label="${tool.name}: GenBank files">
105 <discover_datasets pattern="(?P&lt;name&gt;.+)\.gbff$" directory="./genbanks" format="genbank"/>
106 </collection>
107 <collection name="outputreport" type="list" label="${tool.name}: Report files">
108 <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" directory="./reports" format="txt"/>
109 </collection>
110 <collection name="outputfasta" type="list" label="${tool.name}: FASTA files">
111 <discover_datasets pattern="(?P&lt;name&gt;.+)\.fna$" directory="./assembly" format="fasta"/>
112 </collection>
113
114 <!--<collection name="assemblies" type="list" label="${tool.name} on ${input.element_identifier}: Assembly">
115 <discover_datasets pattern="__name_and_ext__" directory="assembly" />
116 </collection>
117 <collection name="genbanks" type="list" label="${tool.name} on ${input.element_identifier}: GenBank">
118 <discover_datasets pattern="__name_and_ext__" directory="./genbanks" />
119 </collection>-->
120 <!--<data format="html" name="summary_html" label="summary.html"/>-->
121 <data format="tabular" name="summary_tsv" label="${tool.name}: summary.tsv"/>
122 </outputs>
123
124
125 <help><![CDATA[
126 This tool allows to download sequences in FASTA or GenBank format, and retrieve specific information (such as country, pubmed ID, host, ...).
127
128 Please note that NCBI assembly_summary files used to download the sequences have been uploaded on September 6th, 2021.
129
130 To get more recent assembly_summary files, please use the command line or the GUI version of the tool.
131
132 GitHub: https://github.com/karubiotools/getSequenceInfo
133 ]]></help>
134
135 </tool>
136