Mercurial > repos > public-health-bioinformatics > pick_plasmids_containing_genes

annotate pick_plasmids_containing_genes.xml @ 1:c9129ecc609d draft default tip

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
author public-health-bioinformatics
date Thu, 19 Dec 2019 18:22:33 -0500
parents 62019f5116f8
children
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c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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1 <tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" version="0.2.0">
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62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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2 <description>Pick plasmids containing specific genes</description>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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3 <requirements>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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4 </requirements>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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5 <command detect_errors="exit_code"><![CDATA[
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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6 '$__tool_directory__/pick_plasmids_containing_genes.py'
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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7 --plasmids
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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8 #for $plasmid in $plasmids:
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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9 '${plasmid}'
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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10 #end for
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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11 --concatenated_abricate_reports '${concatenated_abricate_reports}'
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c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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12 #if str( $screening_file_source.screening_file_source_selector ) == "tool_data_table":
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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13 #set $input_screening_file = str( $screening_file_source.screening_file.fields.path )
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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14 #else:
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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15 #set $input_screening_file = str( $screening_file_source.screening_file )
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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16 #end if
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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17 --abricate_report_screening_file '${input_screening_file}'
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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18 --outdir outdir &&
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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19 cp '${input_screening_file}' '${output_screening_file}'
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62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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20 ]]></command>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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21 <inputs>
1
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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22 <conditional name="screening_file_source">
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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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?"
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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24 help="Screening files must be stored in the 'abricate_report_screening_files' tool data table">
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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25 <option value="tool_data_table">From tool data table</option>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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26 <option value="history">From history</option>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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27 </param>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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28 <when value="tool_data_table">
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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29 <param name="screening_file" type="select" format="tabular">
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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30 <options from_data_table="abricate_report_screening_files">
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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31 <validator type="no_options" message="No abricate report screening files are available" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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32 </options>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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33 </param>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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34 </when>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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35 <when value="history">
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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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" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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37 </when>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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38 </conditional>
0
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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39 <param name="plasmids" type="data_collection" collection_type="list" format="fasta" />
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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40 <param name="concatenated_abricate_reports" type="data" format="tabular" />
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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41 </inputs>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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42 <outputs>
1
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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43 <collection name="output_plasmids" type="list" label="Output plasmids">
0
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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44 <discover_datasets pattern="__name__" format="fasta" directory="outdir" />
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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45 </collection>
1
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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46 <data name="output_screening_file" format="tabular" />
0
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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47 </outputs>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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48 <tests>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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49 <test>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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50 <param name="plasmids">
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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51 <collection type="list">
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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52 <element name="SRR9113487_plasmid_1068" value="SRR9113487_plasmid_1068.fasta" ftype="fasta" />
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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53 <element name="SRR9113487_plasmid_1550" value="SRR9113487_plasmid_1550.fasta" ftype="fasta" />
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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54 <element name="SRR9113487_plasmid_2719" value="SRR9113487_plasmid_2719.fasta" ftype="fasta" />
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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55 <element name="SRR9113487_plasmid_739" value="SRR9113487_plasmid_739.fasta" ftype="fasta" />
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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56 <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" />
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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57 <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" />
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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58 </collection>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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59 </param>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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60 <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/>
1
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61 <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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62 <param name="screening_file_source.screening_file" value="screening_file_1"/>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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63 <output_collection name="output_plasmids" type="list" count="1" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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64 </test>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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65 <test>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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66 <param name="plasmids">
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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67 <collection type="list">
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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68 <element name="SRR9113487_plasmid_1068" value="SRR9113487_plasmid_1068.fasta" ftype="fasta" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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69 <element name="SRR9113487_plasmid_1550" value="SRR9113487_plasmid_1550.fasta" ftype="fasta" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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70 <element name="SRR9113487_plasmid_2719" value="SRR9113487_plasmid_2719.fasta" ftype="fasta" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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71 <element name="SRR9113487_plasmid_739" value="SRR9113487_plasmid_739.fasta" ftype="fasta" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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72 <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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73 <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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74 </collection>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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75 </param>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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76 <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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77 <param name="screening_file_source.screening_file_source_selector" value="history" />
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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78 <param name="screening_file_source.screening_file" value="abricate_report_screening_file_1.tsv"/>
c9129ecc609d "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit e732b47aa50e35cd4cb70df263d21c5987cae697"
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79 <output_collection name="output_plasmids" type="list" count="1" />
0
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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80 </test>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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81 </tests>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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82 <help><![CDATA[
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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83 ]]></help>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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84 <citations>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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85 </citations>
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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86 </tool>