Mercurial > repos > dfornika > screen_abricate_report

annotate screen_abricate_report.xml @ 1:40003338a8e8 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
author dfornika
date Fri, 27 Sep 2019 13:31:43 -0400
parents 2ffd23634c1e
children 378696e5f81c
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2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.1.0">
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2 <description>Screens an abricate report for genes of interest</description>
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3 <requirements>
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4 </requirements>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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5 <command detect_errors="exit_code"><![CDATA[
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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6 '${__tool_directory__}/screen_abricate_report.py'
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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7 '${abricate_report}'
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8 --screen '${screening_file.fields.path}'
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40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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9 --screened_report '${screened_report}'
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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10 --gene_detection_status '${gene_detection_status}'
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2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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11 ]]></command>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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12 <inputs>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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13 <param name="abricate_report" type="data" format="tabular" />
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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14 <param name="screening_file" type="select" format="tabular">
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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15 <options from_data_table="abricate_report_screening_files">
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16 <validator type="no_options" message="No abricate report screening files are available" />
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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17 </options>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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18 </param>
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19 </inputs>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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20 <outputs>
1
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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21 <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" />
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22 <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="abricate_report" value="abricate_report.tsv"/>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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27 <param name="screen" value="screen.tsv"/>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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28 </test>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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29 </tests>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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30 <help><![CDATA[
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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31 ]]></help>
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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32 <citations>
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33 </citations>
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34 </tool>