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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
author dfornika
date Thu, 02 Jan 2020 21:04:04 +0000
parents 378696e5f81c
children
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2:378696e5f81c 3:1c1c680c70a0
1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.1.0"> 1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.3.0">
2 <description>Screens an abricate report for genes of interest</description> 2 <description>Screens an abricate report for genes of interest</description>
3 <requirements> 3 <requirements>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 '${__tool_directory__}/screen_abricate_report.py' 6 '${__tool_directory__}/screen_abricate_report.py'
7 '${abricate_report}' 7 '${abricate_report}'
8 --screening_file '${screening_file.fields.path}' 8 #if str( $screening_file_source.screening_file_source_selector ) == "tool_data_table":
9 #set $input_screening_file = str( $screening_file_source.screening_file.fields.path )
10 #else:
11 #set $input_screening_file = str( $screening_file_source.screening_file )
12 #end if
13 --screening_file '${input_screening_file}'
9 --screened_report '${screened_report}' 14 --screened_report '${screened_report}'
10 --gene_detection_status '${gene_detection_status}' 15 --gene_detection_status '${gene_detection_status}'
16 --min_coverage '${min_coverage}'
17 --min_identity '${min_identity}' &&
18 cp '${input_screening_file}' '${output_screening_file}'
11 ]]></command> 19 ]]></command>
12 <inputs> 20 <inputs>
21 <conditional name="screening_file_source">
22 <param name="screening_file_source_selector" type="select" label="Select a gene screening file from your history or use one from a tool data table?"
23 help="Screening files must be stored in the 'abricate_report_screening_files' tool data table">
24 <option value="tool_data_table">From tool data table</option>
25 <option value="history">From history</option>
26 </param>
27 <when value="tool_data_table">
28 <param name="screening_file" type="select" format="tabular">
29 <options from_data_table="abricate_report_screening_files">
30 <validator type="no_options" message="No abricate report screening files are available" />
31 </options>
32 </param>
33 </when>
34 <when value="history">
35 <param name="screening_file" type="data" format="tabular" label="Gene screening file" help="A two-column tab-delimited file with gene names and regular expressions" />
36 </when>
37 </conditional>
13 <param name="abricate_report" type="data" format="tabular" /> 38 <param name="abricate_report" type="data" format="tabular" />
14 <param name="screening_file" type="select" format="tabular"> 39 <param name="min_coverage" type="float" min="0.0" value="90.0" max="100.0" />
15 <options from_data_table="abricate_report_screening_files"> 40 <param name="min_identity" type="float" min="0.0" value="90.0" max="100.0" />
16 <validator type="no_options" message="No abricate report screening files are available" />
17 </options>
18 </param>
19 </inputs> 41 </inputs>
20 <outputs> 42 <outputs>
21 <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" /> 43 <data name="screened_report" format="tabular" label="Screened Abricate Report" />
22 <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" /> 44 <data name="gene_detection_status" format="tabular" label="Gene Detection Status" />
45 <data name="output_screening_file" format="tabular" />
23 </outputs> 46 </outputs>
24 <tests> 47 <tests>
25 <test> 48 <test>
26 <param name="abricate_report" value="abricate_report.tsv"/> 49 <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" />
27 <param name="screen" value="screen.tsv"/> 50 <param name="screening_file_source.screening_file" value="test_entry"/>
51 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
52 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
53 <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
54 </test>
55 <test>
56 <param name="screening_file_source.screening_file_source_selector" value="history" />
57 <param name="screening_file_source.screening_file" value="screening_file.tsv"/>
58 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
59 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
60 <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
28 </test> 61 </test>
29 </tests> 62 </tests>
30 <help><![CDATA[ 63 <help><![CDATA[
64 This tool is used to filter (ie. 'screen') an abricate report to only include
65 specific genes of interest.
66
67 A list of genes is supplied in a 'screening file', which is a two-column .tsv
68 with headers 'gene_name' and 'regex'. The first column gives the name of the
69 gene of interest, and the second column is a regular expression that can be used
70 to identify examples of that gene in the 'GENE' column of the abricate report.
71
72 For example, one might use the regex '^KPC-\d+$' to identify all alleles of the
73 KPC gene (KPC-2, KPC-3, KPC-4, ..., KPC-10, ...)
31 ]]></help> 74 ]]></help>
32 <citations> 75 <citations>
33 </citations> 76 </citations>
34 </tool> 77 </tool>