Mercurial > repos > public-health-bioinformatics > screen_abricate_report
view screen_abricate_report.xml @ 2:912a3a3dc082 draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
author | public-health-bioinformatics |
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date | Thu, 19 Dec 2019 20:31:11 -0500 |
parents | 4f963b583186 |
children | 2262e531c50b |
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<tool id="screen_abricate_report" name="Screen Abricate Report" version="0.2.0"> <description>Screens an abricate report for genes of interest</description> <requirements> </requirements> <command detect_errors="exit_code"><![CDATA[ '${__tool_directory__}/screen_abricate_report.py' '${abricate_report}' #if str( $screening_file_source.screening_file_source_selector ) == "tool_data_table": #set $input_screening_file = str( $screening_file_source.screening_file.fields.path ) #else: #set $input_screening_file = str( $screening_file_source.screening_file ) #end if --screening_file '${input_screening_file}' --screened_report '${screened_report}' --gene_detection_status '${gene_detection_status}' && cp '${input_screening_file}' '${output_screening_file}' ]]></command> <inputs> <conditional name="screening_file_source"> <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?" help="Screening files must be stored in the 'abricate_report_screening_files' tool data table"> <option value="tool_data_table">From tool data table</option> <option value="history">From history</option> </param> <when value="tool_data_table"> <param name="screening_file" type="select" format="tabular"> <options from_data_table="abricate_report_screening_files"> <validator type="no_options" message="No abricate report screening files are available" /> </options> </param> </when> <when value="history"> <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" /> </when> </conditional> <param name="abricate_report" type="data" format="tabular" /> </inputs> <outputs> <data name="screened_report" format="tabular" label="Screened Abricate Report" /> <data name="gene_detection_status" format="tabular" label="Gene Detection Status" /> <data name="output_screening_file" format="tabular" /> </outputs> <tests> <test> <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" /> <param name="screening_file_source.screening_file" value="test_entry"/> <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/> <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/> <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/> </test> <test> <param name="screening_file_source.screening_file_source_selector" value="history" /> <param name="screening_file_source.screening_file" value="screening_file.tsv"/> <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/> <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/> <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/> </test> </tests> <help><![CDATA[ This tool is used to filter (ie. 'screen') an abricate report to only include specific genes of interest. A list of genes is supplied in a 'screening file', which is a two-column .tsv with headers 'gene_name' and 'regex'. The first column gives the name of the gene of interest, and the second column is a regular expression that can be used to identify examples of that gene in the 'GENE' column of the abricate report. For example, one might use the regex 'KPC\-{d+}' to identify all alleles of the KPC gene (KPC-2, KPC-3, KPC-4, ..., KPC-10, ...) ]]></help> <citations> </citations> </tool>