Mercurial > repos > public-health-bioinformatics > pick_plasmids_containing_genes
comparison pick_plasmids_containing_genes.xml @ 1:c9129ecc609d draft default tip
"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 |
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date | Thu, 19 Dec 2019 18:22:33 -0500 |
parents | 62019f5116f8 |
children |
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0:62019f5116f8 | 1:c9129ecc609d |
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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> |