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 ae10b1f55b2356bea735a994619288f7575430cb"
author public-health-bioinformatics
date Fri, 03 Jan 2020 14:30:22 -0500
parents 2262e531c50b
children
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22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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1 <tool id="screen_abricate_report" name="Screen Abricate Report" version="0.4.0+galaxy0">
0
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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2 <description>Screens an abricate report for genes of interest</description>
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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3 <requirements>
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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4 </requirements>
4
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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5 <version_command><![CDATA[screen_abricate_report.py --version]]></version_command>
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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6 <command detect_errors="exit_code"><![CDATA[
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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7 '${__tool_directory__}/screen_abricate_report.py'
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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8 '${abricate_report}'
2
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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9 #if str( $screening_file_source.screening_file_source_selector ) == "tool_data_table":
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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10 #set $input_screening_file = str( $screening_file_source.screening_file.fields.path )
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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11 #else:
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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12 #set $input_screening_file = str( $screening_file_source.screening_file )
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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13 #end if
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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14 --screening_file '${input_screening_file}'
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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15 --screened_report '${screened_report}'
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2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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16 --gene_detection_status '${gene_detection_status}'
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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17 --min_coverage '${min_coverage}'
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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18 --min_identity '${min_identity}' &&
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19 cp '${input_screening_file}' '${output_screening_file}'
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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20 ]]></command>
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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21 <inputs>
2
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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22 <conditional name="screening_file_source">
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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23 <param name="screening_file_source_selector" type="select" label="Select a gene screening file from your history or use one from a tool data table?"
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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24 help="Screening files must be stored in the 'abricate_report_screening_files' tool data table">
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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25 <option value="tool_data_table">From tool data table</option>
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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26 <option value="history">From history</option>
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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27 </param>
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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28 <when value="tool_data_table">
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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29 <param name="screening_file" type="select" format="tabular">
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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30 <options from_data_table="abricate_report_screening_files">
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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31 <validator type="no_options" message="No abricate report screening files are available" />
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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32 </options>
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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33 </param>
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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34 </when>
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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35 <when value="history">
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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36 <param name="screening_file" type="data" format="tabular" label="Gene screening file" help="A two-column tab-delimited file with gene names and regular expressions" />
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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37 </when>
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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38 </conditional>
0
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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39 <param name="abricate_report" type="data" format="tabular" />
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2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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40 <param name="min_coverage" type="float" min="0.0" value="90.0" max="100.0" />
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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41 <param name="min_identity" type="float" min="0.0" value="90.0" max="100.0" />
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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42 </inputs>
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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43 <outputs>
1
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44 <data name="screened_report" format="tabular" label="Screened Abricate Report" />
4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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45 <data name="gene_detection_status" format="tabular" label="Gene Detection Status" />
2
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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46 <data name="output_screening_file" format="tabular" />
0
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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47 </outputs>
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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48 <tests>
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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49 <test>
2
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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50 <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" />
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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51 <param name="screening_file_source.screening_file" value="test_entry"/>
4
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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52 <param name="abricate_report" value="SAMN13042171-abricate_report_full.tsv"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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53 <output name="screened_report" file="SAMN13042171-abricate_report_screened.tsv" ftype="tabular"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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54 <output name="gene_detection_status" file="SAMN13042171-gene_detection_status.tsv" ftype="tabular"/>
2
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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55 </test>
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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56 <test>
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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57 <param name="screening_file_source.screening_file_source_selector" value="history" />
912a3a3dc082 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467"
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58 <param name="screening_file_source.screening_file" value="screening_file.tsv"/>
4
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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59 <param name="abricate_report" value="SAMN13042171-abricate_report_full.tsv"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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60 <output name="screened_report" file="SAMN13042171-abricate_report_screened.tsv" ftype="tabular"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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61 <output name="gene_detection_status" file="SAMN13042171-gene_detection_status.tsv" ftype="tabular"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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62 </test>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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63 <test>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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64 <param name="screening_file_source.screening_file_source_selector" value="history" />
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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65 <param name="screening_file_source.screening_file" value="screening_file.tsv"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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66 <param name="abricate_report" value="SAMN11840202-abricate_report_full.tsv"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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67 <output name="screened_report" file="SAMN11840202-abricate_report_screened.tsv" ftype="tabular"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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68 <output name="gene_detection_status" file="SAMN11840202-gene_detection_status.tsv" ftype="tabular"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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69 </test>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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70 <test>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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71 <param name="screening_file_source.screening_file_source_selector" value="history" />
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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72 <param name="screening_file_source.screening_file" value="screening_file.tsv"/>
22247b1a59d5 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
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73 <param name="abricate_report" value="SAMN11840203-abricate_report_full.tsv"/>
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74 <output name="screened_report" file="SAMN11840203-abricate_report_screened.tsv" ftype="tabular"/>
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75 <output name="gene_detection_status" file="SAMN11840203-gene_detection_status.tsv" ftype="tabular"/>
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76 </test>
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77 </tests>
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78 <help><![CDATA[
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79 This tool is used to filter (ie. 'screen') an abricate report to only include
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80 specific genes of interest.
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81
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82 A list of genes is supplied in a 'screening file', which is a two-column .tsv
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83 with headers 'gene_name' and 'regex'. The first column gives the name of the
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84 gene of interest, and the second column is a regular expression that can be used
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85 to identify examples of that gene in the 'GENE' column of the abricate report.
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86
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87 For example, one might use the regex '^KPC-\d+$' to identify all alleles of the
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88 KPC gene (KPC-2, KPC-3, KPC-4, ..., KPC-10, ...)
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89 ]]></help>
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90 <citations>
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91 </citations>
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92 </tool>