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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
comparison
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0:62019f5116f8 1:c9129ecc609d
1 <tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" version="0.1.0"> 1 <tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" version="0.2.0">
2 <description>Pick plasmids containing specific genes</description> 2 <description>Pick plasmids containing specific genes</description>
3 <requirements> 3 <requirements>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 '$__tool_directory__/pick_plasmids_containing_genes.py' 6 '$__tool_directory__/pick_plasmids_containing_genes.py'
7 --plasmids 7 --plasmids
8 #for $plasmid in $plasmids: 8 #for $plasmid in $plasmids:
9 '${plasmid}' 9 '${plasmid}'
10 #end for 10 #end for
11 --concatenated_abricate_reports '${concatenated_abricate_reports}' 11 --concatenated_abricate_reports '${concatenated_abricate_reports}'
12 --abricate_report_screening_file '${screening_file.fields.path}' 12 #if str( $screening_file_source.screening_file_source_selector ) == "tool_data_table":
13 --outdir outdir 13 #set $input_screening_file = str( $screening_file_source.screening_file.fields.path )
14 #else:
15 #set $input_screening_file = str( $screening_file_source.screening_file )
16 #end if
17 --abricate_report_screening_file '${input_screening_file}'
18 --outdir outdir &&
19 cp '${input_screening_file}' '${output_screening_file}'
14 ]]></command> 20 ]]></command>
15 <inputs> 21 <inputs>
22 <conditional name="screening_file_source">
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?"
24 help="Screening files must be stored in the 'abricate_report_screening_files' tool data table">
25 <option value="tool_data_table">From tool data table</option>
26 <option value="history">From history</option>
27 </param>
28 <when value="tool_data_table">
29 <param name="screening_file" type="select" format="tabular">
30 <options from_data_table="abricate_report_screening_files">
31 <validator type="no_options" message="No abricate report screening files are available" />
32 </options>
33 </param>
34 </when>
35 <when value="history">
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" />
37 </when>
38 </conditional>
16 <param name="plasmids" type="data_collection" collection_type="list" format="fasta" /> 39 <param name="plasmids" type="data_collection" collection_type="list" format="fasta" />
17 <param name="concatenated_abricate_reports" type="data" format="tabular" /> 40 <param name="concatenated_abricate_reports" type="data" format="tabular" />
18 <param name="screening_file" type="select" format="tabular">
19 <options from_data_table="abricate_report_screening_files">
20 <validator type="no_options" message="No abricate report screening files are available" />
21 </options>
22 </param>
23 </inputs> 41 </inputs>
24 <outputs> 42 <outputs>
25 <collection name="output" type="list" label="Output plasmids"> 43 <collection name="output_plasmids" type="list" label="Output plasmids">
26 <discover_datasets pattern="__name__" format="fasta" directory="outdir" /> 44 <discover_datasets pattern="__name__" format="fasta" directory="outdir" />
27 </collection> 45 </collection>
46 <data name="output_screening_file" format="tabular" />
28 </outputs> 47 </outputs>
29 <tests> 48 <tests>
30 <test> 49 <test>
31 <param name="plasmids"> 50 <param name="plasmids">
32 <collection type="list"> 51 <collection type="list">
37 <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" /> 56 <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" />
38 <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" /> 57 <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" />
39 </collection> 58 </collection>
40 </param> 59 </param>
41 <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/> 60 <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/>
42 <param name="screening_file" value="screening_file_1"/> 61 <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" />
43 <output file="outdir/SRR9113487_plasmid_2719.fasta" ftype="fasta"/> 62 <param name="screening_file_source.screening_file" value="screening_file_1"/>
63 <output_collection name="output_plasmids" type="list" count="1" />
64 </test>
65 <test>
66 <param name="plasmids">
67 <collection type="list">
68 <element name="SRR9113487_plasmid_1068" value="SRR9113487_plasmid_1068.fasta" ftype="fasta" />
69 <element name="SRR9113487_plasmid_1550" value="SRR9113487_plasmid_1550.fasta" ftype="fasta" />
70 <element name="SRR9113487_plasmid_2719" value="SRR9113487_plasmid_2719.fasta" ftype="fasta" />
71 <element name="SRR9113487_plasmid_739" value="SRR9113487_plasmid_739.fasta" ftype="fasta" />
72 <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" />
73 <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" />
74 </collection>
75 </param>
76 <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/>
77 <param name="screening_file_source.screening_file_source_selector" value="history" />
78 <param name="screening_file_source.screening_file" value="abricate_report_screening_file_1.tsv"/>
79 <output_collection name="output_plasmids" type="list" count="1" />
44 </test> 80 </test>
45 </tests> 81 </tests>
46 <help><![CDATA[ 82 <help><![CDATA[
47 ]]></help> 83 ]]></help>
48 <citations> 84 <citations>