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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
author public-health-bioinformatics
date Fri, 03 Jan 2020 14:30:22 -0500
parents 2262e531c50b
children
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3:2262e531c50b 4:22247b1a59d5
1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.3.0"> 1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.4.0+galaxy0">
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 <version_command><![CDATA[screen_abricate_report.py --version]]></version_command>
5 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
6 '${__tool_directory__}/screen_abricate_report.py' 7 '${__tool_directory__}/screen_abricate_report.py'
7 '${abricate_report}' 8 '${abricate_report}'
8 #if str( $screening_file_source.screening_file_source_selector ) == "tool_data_table": 9 #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 #set $input_screening_file = str( $screening_file_source.screening_file.fields.path )
46 </outputs> 47 </outputs>
47 <tests> 48 <tests>
48 <test> 49 <test>
49 <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" /> 50 <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" />
50 <param name="screening_file_source.screening_file" value="test_entry"/> 51 <param name="screening_file_source.screening_file" value="test_entry"/>
51 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/> 52 <param name="abricate_report" value="SAMN13042171-abricate_report_full.tsv"/>
52 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/> 53 <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 <output name="gene_detection_status" file="SAMN13042171-gene_detection_status.tsv" ftype="tabular"/>
54 </test> 55 </test>
55 <test> 56 <test>
56 <param name="screening_file_source.screening_file_source_selector" value="history" /> 57 <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="screening_file_source.screening_file" value="screening_file.tsv"/>
58 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/> 59 <param name="abricate_report" value="SAMN13042171-abricate_report_full.tsv"/>
59 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/> 60 <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"/> 61 <output name="gene_detection_status" file="SAMN13042171-gene_detection_status.tsv" ftype="tabular"/>
62 </test>
63 <test>
64 <param name="screening_file_source.screening_file_source_selector" value="history" />
65 <param name="screening_file_source.screening_file" value="screening_file.tsv"/>
66 <param name="abricate_report" value="SAMN11840202-abricate_report_full.tsv"/>
67 <output name="screened_report" file="SAMN11840202-abricate_report_screened.tsv" ftype="tabular"/>
68 <output name="gene_detection_status" file="SAMN11840202-gene_detection_status.tsv" ftype="tabular"/>
69 </test>
70 <test>
71 <param name="screening_file_source.screening_file_source_selector" value="history" />
72 <param name="screening_file_source.screening_file" value="screening_file.tsv"/>
73 <param name="abricate_report" value="SAMN11840203-abricate_report_full.tsv"/>
74 <output name="screened_report" file="SAMN11840203-abricate_report_screened.tsv" ftype="tabular"/>
75 <output name="gene_detection_status" file="SAMN11840203-gene_detection_status.tsv" ftype="tabular"/>
61 </test> 76 </test>
62 </tests> 77 </tests>
63 <help><![CDATA[ 78 <help><![CDATA[
64 This tool is used to filter (ie. 'screen') an abricate report to only include 79 This tool is used to filter (ie. 'screen') an abricate report to only include
65 specific genes of interest. 80 specific genes of interest.