Mercurial > repos > public-health-bioinformatics > screen_abricate_report

comparison screen_abricate_report.xml @ 0:b2d56a44a872 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
author public-health-bioinformatics
date Thu, 31 Oct 2019 15:43:15 -0400
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children 4f963b583186
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-1:000000000000 0:b2d56a44a872
1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.1.0">
2 <description>Screens an abricate report for genes of interest</description>
3 <requirements>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 '${__tool_directory__}/screen_abricate_report.py'
7 '${abricate_report}'
8 --screening_file '${screening_file.fields.path}'
9 --screened_report '${screened_report}'
10 --gene_detection_status '${gene_detection_status}'
11 ]]></command>
12 <inputs>
13 <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>
20 <outputs>
21 <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" />
22 <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" />
23 </outputs>
24 <tests>
25 <test>
26 <param name="screening_file" value="test_entry"/>
27 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
28 <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"/>
30 </test>
31 </tests>
32 <help><![CDATA[
33 ]]></help>
34 <citations>
35 </citations>
36 </tool>