Mercurial > repos > public-health-bioinformatics > screen_abricate_report

comparison screen_abricate_report.xml @ 3:2262e531c50b draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
author public-health-bioinformatics
date Thu, 02 Jan 2020 17:14:34 -0500
parents 912a3a3dc082
children 22247b1a59d5
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2:912a3a3dc082 3:2262e531c50b
1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.2.0"> 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'
10 #else: 10 #else:
11 #set $input_screening_file = str( $screening_file_source.screening_file ) 11 #set $input_screening_file = str( $screening_file_source.screening_file )
12 #end if 12 #end if
13 --screening_file '${input_screening_file}' 13 --screening_file '${input_screening_file}'
14 --screened_report '${screened_report}' 14 --screened_report '${screened_report}'
15 --gene_detection_status '${gene_detection_status}' && 15 --gene_detection_status '${gene_detection_status}'
16 --min_coverage '${min_coverage}'
17 --min_identity '${min_identity}' &&
16 cp '${input_screening_file}' '${output_screening_file}' 18 cp '${input_screening_file}' '${output_screening_file}'
17 ]]></command> 19 ]]></command>
18 <inputs> 20 <inputs>
19 <conditional name="screening_file_source"> 21 <conditional name="screening_file_source">
20 <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?" 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?"
32 <when value="history"> 34 <when value="history">
33 <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" /> 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" />
34 </when> 36 </when>
35 </conditional> 37 </conditional>
36 <param name="abricate_report" type="data" format="tabular" /> 38 <param name="abricate_report" type="data" format="tabular" />
39 <param name="min_coverage" type="float" min="0.0" value="90.0" max="100.0" />
40 <param name="min_identity" type="float" min="0.0" value="90.0" max="100.0" />
37 </inputs> 41 </inputs>
38 <outputs> 42 <outputs>
39 <data name="screened_report" format="tabular" label="Screened Abricate Report" /> 43 <data name="screened_report" format="tabular" label="Screened Abricate Report" />
40 <data name="gene_detection_status" format="tabular" label="Gene Detection Status" /> 44 <data name="gene_detection_status" format="tabular" label="Gene Detection Status" />
41 <data name="output_screening_file" format="tabular" /> 45 <data name="output_screening_file" format="tabular" />
63 A list of genes is supplied in a 'screening file', which is a two-column .tsv 67 A list of genes is supplied in a 'screening file', which is a two-column .tsv
64 with headers 'gene_name' and 'regex'. The first column gives the name of the 68 with headers 'gene_name' and 'regex'. The first column gives the name of the
65 gene of interest, and the second column is a regular expression that can be used 69 gene of interest, and the second column is a regular expression that can be used
66 to identify examples of that gene in the 'GENE' column of the abricate report. 70 to identify examples of that gene in the 'GENE' column of the abricate report.
67 71
68 For example, one might use the regex 'KPC\-{d+}' to identify all alleles of the 72 For example, one might use the regex '^KPC-\d+$' to identify all alleles of the
69 KPC gene (KPC-2, KPC-3, KPC-4, ..., KPC-10, ...) 73 KPC gene (KPC-2, KPC-3, KPC-4, ..., KPC-10, ...)
70 ]]></help> 74 ]]></help>
71 <citations> 75 <citations>
72 </citations> 76 </citations>
73 </tool> 77 </tool>