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comparison screen_abricate_report.xml @ 2:912a3a3dc082 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
author public-health-bioinformatics
date Thu, 19 Dec 2019 20:31:11 -0500
parents 4f963b583186
children 2262e531c50b
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1:4f963b583186 2:912a3a3dc082
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="0.2.0">
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 cp '${input_screening_file}' '${output_screening_file}'
11 ]]></command> 17 ]]></command>
12 <inputs> 18 <inputs>
19 <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?"
21 help="Screening files must be stored in the 'abricate_report_screening_files' tool data table">
22 <option value="tool_data_table">From tool data table</option>
23 <option value="history">From history</option>
24 </param>
25 <when value="tool_data_table">
26 <param name="screening_file" type="select" format="tabular">
27 <options from_data_table="abricate_report_screening_files">
28 <validator type="no_options" message="No abricate report screening files are available" />
29 </options>
30 </param>
31 </when>
32 <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" />
34 </when>
35 </conditional>
13 <param name="abricate_report" type="data" format="tabular" /> 36 <param name="abricate_report" type="data" format="tabular" />
14 <param name="screening_file" type="select" format="tabular">
15 <options from_data_table="abricate_report_screening_files">
16 <validator type="no_options" message="No abricate report screening files are available" />
17 </options>
18 </param>
19 </inputs> 37 </inputs>
20 <outputs> 38 <outputs>
21 <data name="screened_report" format="tabular" label="Screened Abricate Report" /> 39 <data name="screened_report" format="tabular" label="Screened Abricate Report" />
22 <data name="gene_detection_status" format="tabular" label="Gene Detection Status" /> 40 <data name="gene_detection_status" format="tabular" label="Gene Detection Status" />
41 <data name="output_screening_file" format="tabular" />
23 </outputs> 42 </outputs>
24 <tests> 43 <tests>
25 <test> 44 <test>
26 <param name="screening_file" value="test_entry"/> 45 <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" />
46 <param name="screening_file_source.screening_file" value="test_entry"/>
47 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
48 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
49 <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
50 </test>
51 <test>
52 <param name="screening_file_source.screening_file_source_selector" value="history" />
53 <param name="screening_file_source.screening_file" value="screening_file.tsv"/>
27 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/> 54 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
28 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/> 55 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
29 <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/> 56 <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
30 </test> 57 </test>
31 </tests> 58 </tests>
32 <help><![CDATA[ 59 <help><![CDATA[
60 This tool is used to filter (ie. 'screen') an abricate report to only include
61 specific genes of interest.
62
63 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
65 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.
67
68 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, ...)
33 ]]></help> 70 ]]></help>
34 <citations> 71 <citations>
35 </citations> 72 </citations>
36 </tool> 73 </tool>