Mercurial > repos > public-health-bioinformatics > screen_abricate_report
comparison screen_abricate_report.xml @ 4:22247b1a59d5 draft default tip
"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 |
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| 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. |