Mercurial > repos > public-health-bioinformatics > screen_abricate_report

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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 15:14:36 -0400
parents 2c6153023368
children
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2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.1.0">
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
public-health-bioinformatics
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2 <description>Screens an abricate report for genes of interest</description>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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3 <requirements>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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4 </requirements>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
public-health-bioinformatics
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5 <command detect_errors="exit_code"><![CDATA[
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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6 '${__tool_directory__}/screen_abricate_report.py'
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
public-health-bioinformatics
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7 '${abricate_report}'
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
public-health-bioinformatics
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8 --screening_file '${screening_file.fields.path}'
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
public-health-bioinformatics
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9 --screened_report '${screened_report}'
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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10 --gene_detection_status '${gene_detection_status}'
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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11 ]]></command>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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12 <inputs>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
public-health-bioinformatics
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13 <param name="abricate_report" type="data" format="tabular" />
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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14 <param name="screening_file" type="select" format="tabular">
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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15 <options from_data_table="abricate_report_screening_files">
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
public-health-bioinformatics
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16 <validator type="no_options" message="No abricate report screening files are available" />
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
public-health-bioinformatics
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17 </options>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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18 </param>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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19 </inputs>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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20 <outputs>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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21 <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" />
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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22 <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" />
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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23 </outputs>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
public-health-bioinformatics
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24 <tests>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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25 <test>
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45542cd244ad "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
public-health-bioinformatics
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26 <param name="screening_file" value="test_entry"/>
45542cd244ad "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
public-health-bioinformatics
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27 <param name="abricate_report" value="SAMN13042171_abricate_report.tsv"/>
45542cd244ad "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
public-health-bioinformatics
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28 <output name="screened_report" file="SAMN13042171_abricate_report_screened.tsv" ftype="tabular"/>
45542cd244ad "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
public-health-bioinformatics
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29 <output name="gene_detection_status" file="SAMN13042171_gene_detection_status.tsv" ftype="tabular"/>
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2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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30 </test>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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31 </tests>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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32 <help><![CDATA[
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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33 ]]></help>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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34 <citations>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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35 </citations>
2c6153023368 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"
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36 </tool>