Mercurial > repos > greg > draw_amr_matrix
comparison draw_amr_matrix.xml @ 13:b1a7e04e6371 draft
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author | greg |
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date | Tue, 28 Mar 2023 13:21:09 +0000 |
parents | da1c9c1be421 |
children | c5e80637cf3d |
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12:aa2b737102dc | 13:b1a7e04e6371 |
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40 --amr_matrix_png_dir 'amr_matrix_png_dir' | 40 --amr_matrix_png_dir 'amr_matrix_png_dir' |
41 --errors '$errors' | 41 --errors '$errors' |
42 #if str($output_process_log) == 'yes': | 42 #if str($output_process_log) == 'yes': |
43 && mv 'process_log' '$process_log' | 43 && mv 'process_log' '$process_log' |
44 #end if | 44 #end if |
45 --in_test_mode '$in_test_mode' | |
45 ]]></command> | 46 ]]></command> |
46 <inputs> | 47 <inputs> |
47 <conditional name="reference_source"> | 48 <conditional name="reference_source"> |
48 <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a cached genome index?"> | 49 <param name="reference_source_selector" type="select" label="Select a reference genome from your history or use a cached genome index?"> |
49 <option value="cached">Use a cached genome index</option> | 50 <option value="cached">Use a cached genome index</option> |
68 <param argument="--amr_gene_drug_file" type="data" format="tabular,tsv" label="AMR gene drugs file"/> | 69 <param argument="--amr_gene_drug_file" type="data" format="tabular,tsv" label="AMR gene drugs file"/> |
69 <param name="output_process_log" type="select" display="radio" label="Output process log file?"> | 70 <param name="output_process_log" type="select" display="radio" label="Output process log file?"> |
70 <option value="no" selected="true">No</option> | 71 <option value="no" selected="true">No</option> |
71 <option value="yes">Yes</option> | 72 <option value="yes">Yes</option> |
72 </param> | 73 </param> |
74 <param name="in_test_mode" type="hidden" value="false"/> | |
73 </inputs> | 75 </inputs> |
74 <outputs> | 76 <outputs> |
75 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> | 77 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> |
76 <filter>output_process_log == 'yes'</filter> | 78 <filter>output_process_log == 'yes'</filter> |
77 </data> | 79 </data> |
94 </collection> | 96 </collection> |
95 </param> | 97 </param> |
96 <param name="varscan_vcf_file" value="varscan.vcf" ftype="vcf"/> | 98 <param name="varscan_vcf_file" value="varscan.vcf" ftype="vcf"/> |
97 <param name="amr_mutation_regions_bed_file" value="amr_mutation_regions.bed" ftype="bed"/> | 99 <param name="amr_mutation_regions_bed_file" value="amr_mutation_regions.bed" ftype="bed"/> |
98 <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/> | 100 <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/> |
101 <param name="in_test_mode" value="true"/> | |
99 <output_collection name="amr_matrix_png" type="list" count="1"> | 102 <output_collection name="amr_matrix_png" type="list" count="1"> |
100 <element name="amr_matrix" ftype="png"> | 103 <element name="amr_matrix" ftype="png"> |
101 <assert_contents> | 104 <assert_contents> |
102 <has_size value="28798" delta="1000"/> | 105 <has_size value="28798" delta="1000"/> |
103 </assert_contents> | 106 </assert_contents> |