Mercurial > repos > public-health-bioinformatics > pick_plasmids_containing_genes

annotate pick_plasmids_containing_genes.xml @ 0:62019f5116f8 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
author public-health-bioinformatics
date Tue, 12 Nov 2019 22:20:54 -0500
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children c9129ecc609d
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0
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
public-health-bioinformatics
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1 <tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" version="0.1.0">
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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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"
public-health-bioinformatics
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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 '${concatenated_abricate_reports}'
62019f5116f8 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit af16cdb29dcdc9ad2ff1effb5cf4e23a8c98a764"
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12 --abricate_report_screening_file '${screening_file.fields.path}'
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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13 --outdir 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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14 ]]></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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15 <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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16 <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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17 <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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18 <param name="screening_file" type="select" 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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19 <options from_data_table="abricate_report_screening_files">
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 <validator type="no_options" message="No abricate report screening files are available" />
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 </options>
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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22 </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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23 </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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24 <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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25 <collection name="output" type="list" label="Output 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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26 <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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27 </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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28 </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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29 <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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30 <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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31 <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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32 <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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33 <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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34 <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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35 <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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36 <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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37 <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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38 <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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39 </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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40 </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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41 <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="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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42 <param name="screening_file" value="screening_file_1"/>
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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43 <output file="outdir/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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44 </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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45 </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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46 <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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47 ]]></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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48 <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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49 </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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50 </tool>