Mercurial > repos > iuc > plasmidfinder

comparison plasmidfinder.xml @ 0:2b6e795b22a9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/plasmidfinder commit 32b1446d0da698b945d7f8b5df6d251b9989d3b1
author iuc
date Mon, 19 Sep 2022 08:47:42 +0000
parents
children eccc7495c3d9
comparison
equal deleted inserted replaced
-1:000000000000 0:2b6e795b22a9
1 <tool id="plasmidfinder" name="PlasmidFinder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>
3 Plasmid identification in bacteria.
4 </description>
5 <macros>
6 <import>macro.xml</import>
7 </macros>
8 <expand macro='xrefs'/>
9 <expand macro="requirements" />
10 <command detect_errors="aggressive"><![CDATA[
11 mkdir output_dir &&
12 mkdir temp_dir &&
13 plasmidfinder.py
14 -i '$input.input_file'
15 -p '$input.database_name.fields.path'
16 -l '$options.min_cov'
17 -t '$options.threshold'
18 #if $input.input_file.ext == 'fasta' or $input.input_file.ext == 'fasta.gz'
19 -mp blastn
20 #else if $input.input_file.ext == 'fastqsanger.gz' or $input.input_file.ext == 'fastqsanger'
21 -mp kma
22 #end if
23 -x
24 -o output_dir
25 -tmp temp_dir
26 #*======================================
27 LOG file
28 ======================================*#
29 | tee '$log_file'
30 ]]>
31 </command>
32 <inputs>
33 <section name="input" title="Input parameters" expanded="true">
34 <param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Choose a fasta or fastq file" help="File to be analyzed"/>
35 <param name="database_name" type="select" label="PlasmidFinder database">
36 <options from_data_table="plasmidfinder_db">
37 <validator message="No PlasmidFinder database is available" type="no_options"/>
38 </options>
39 </param>
40 </section>
41 <section name="options" title="Options">
42 <param name="min_cov" type="float" min="0" max="1" value="0.6" label="Minimal coverage" help="Choose a minimum coverage value (default: 0.6)"/>
43 <param name="threshold" type="float" min="0" max="1" value="0.95" label="Minimal identity" help="Choose a minimum identity value (default: 0.95)"/>
44 </section>
45 <section name="output_files" title="Output file selection">
46 <param name="output_selection" type="select" display="checkboxes" multiple="true" label="Output files selection">
47 <option value="data_json">JSON file result</option>
48 <option value="hit_fasta" selected="true">Hits in genome</option>
49 <option value="plasmid_fasta" selected="true">Plasmid hits</option>
50 <option value="result_tsv" selected="true">Plasmid results</option>
51 <option value="result_txt" selected="true">Raw results</option>
52 <option value="logfile">Log file</option>
53 </param>
54 </section>
55 </inputs>
56 <outputs>
57 <data name="json_file" format="json" from_work_dir="output_dir/data.json" label="${tool.name} on ${on_string}: data.json">
58 <filter> "data_json" in output_files['output_selection'] </filter>
59 </data>
60 <data name="hit_file" format="fasta" from_work_dir="output_dir/Hit_in_genome_seq.fsa" label="${tool.name} on ${on_string}: hit_in_genome.fasta">
61 <filter> "hit_fasta" in output_files['output_selection'] </filter>
62 </data>
63 <data name="plasmid_file" format="fasta" from_work_dir="output_dir/Plasmid_seqs.fsa" label="${tool.name} on ${on_string}: plasmid.fasta">
64 <filter> "plasmid_fasta" in output_files['output_selection'] </filter>
65 </data>
66 <data name="result_file" format="tabular" from_work_dir="output_dir/results_tab.tsv" label="${tool.name} on ${on_string}: results.tsv">
67 <filter> "result_tsv" in output_files['output_selection'] </filter>
68 </data>
69 <data name="raw_file" format="txt" from_work_dir="output_dir/results.txt" label="${tool.name} on ${on_string}: raw_result.txt">
70 <filter> "result_txt" in output_files['output_selection'] </filter>
71 </data>
72 <data name="log_file" format="txt" from_work_dir="output_dir" label="${tool.name} on ${on_string}: log file">
73 <filter> "logfile" in output_files['output_selection'] </filter>
74 </data>
75 </outputs>
76 <tests>
77 <!--test_1 with default value and all output files for contigs -->
78 <test expect_num_outputs="6">
79 <section name="input">
80 <param name="input_file" value="contigs.fasta"/>
81 <param name="input_type" value="genome"/>
82 <param name="database_name" value="test-plasmindfinder-db"/>
83 </section>
84 <section name="output_files">
85 <param name="output_selection" value="data_json,hit_fasta,plasmid_fasta,result_tsv,result_txt,logfile"/>
86 </section>
87 <output name="json_file" value="test_1/data_test1.json" ftype="json" compare="sim_size"/>
88 <output name="hit_file" value="test_1/Hit_in_genome_seq_test1.fsa" ftype="fasta"/>
89 <output name="plasmid_file" value="test_1/Plasmid_seqs_test1.fsa" ftype="fasta"/>
90 <output name="result_file" value="test_1/results_tab_test1.tsv"/>
91 <output name="raw_file" value="test_1/results_test1.txt" lines_diff="2"/>
92 <output name="log_file" value="test_1/logfile_test1.log" lines_diff="7"/>
93 </test>
94 <!--test_2 with default value and for fastq file -->
95 <test expect_num_outputs="4">
96 <section name="input">
97 <param name="input_file" value="data.fastq.gz"/>
98 <param name="input_type" value="raw"/>
99 <param name="database_name" value="test-plasmindfinder-db"/>
100 </section>
101 <section name="output_files">
102 <param name="output_selection" value="data_json,result_tsv,result_txt,logfile"/>
103 </section>
104 <output name="json_file" value="test_2/data_test2.json" ftype="json" compare="sim_size"/>
105 <output name="result_file" value="test_2/results_tab_test2.tsv"/>
106 <output name="raw_file" value="test_2/results_test2.txt" lines_diff="2"/>
107 <output name="log_file" value="test_2/logfile_test2.log" lines_diff="7"/>
108 </test>
109 <!--test_3 with default value and for fastq file -->
110 <test expect_num_outputs="3">
111 <section name="input">
112 <param name="input_file" value="contigs.fasta"/>
113 <param name="input_type" value="genome"/>
114 <param name="database_name" value="test-plasmindfinder-db"/>
115 </section>
116 <section name="options">
117 <param name="min_cov" value="0.2" />
118 <param name="threshold" value="0.6"/>
119 </section>
120 <section name="output_files">
121 <param name="output_selection" value="hit_fasta,plasmid_fasta,result_tsv"/>
122 </section>
123 <output name="hit_file" value="test_3/Hit_in_genome_seq_test3.fsa" ftype="fasta"/>
124 <output name="plasmid_file" value="test_3/Plasmid_seqs_test3.fsa" ftype="fasta"/>
125 <output name="result_file" value="test_3/results_tab_test3.tsv"/>
126 </test>
127 </tests>
128 <help><![CDATA[
129 **What it does**
130 PlasmidFinder characterize plasmid sequences into whole genome sequencing.
131 It is based on [plasmidfinder database](https://bitbucket.org/genomicepidemiology/plasmidfinder_db/) with hundreds sequences.
132 **Input**
133 It can analyse raw data using a k-mer approach based on KMA or a blastn for genome assembly.
134 A database is need obtained from the plasmidfinder database.
135 **Options**
136 You can modify the coverage value (% of matching sequence on the total target sequence)
137 You can modify the identity threshold (% of shared nucleotide on the match)
138 **Output**
139 Some output files are availables
140 - A fasta file with all available hits detected in the genome
141 - A fasta file with all plasmid sequences from the database
142 - A summary of the analysis in tabular format
143 - A Raw result file in text format
144 - A JSON file could be use for other boinformatic analaysis
145 - A log file with analysis parameters
146
147 ]]></help>
148 <expand macro="citations"/>
149 </tool>