Mercurial > repos > greg > draw_amr_matrix
comparison draw_amr_matrix.xml @ 9:70073df30a06 draft
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author | greg |
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date | Tue, 21 Mar 2023 14:06:11 +0000 |
parents | 389c98d344ce |
children | da1c9c1be421 |
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8:7fe8ea50a81d | 9:70073df30a06 |
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36 --mutation_regions_dir 'mutation_regions_dir' | 36 --mutation_regions_dir 'mutation_regions_dir' |
37 #end if | 37 #end if |
38 --amr_gene_drug_file '$amr_gene_drug_file' | 38 --amr_gene_drug_file '$amr_gene_drug_file' |
39 --reference_genome reference.fa | 39 --reference_genome reference.fa |
40 --amr_matrix_png_dir 'amr_matrix_png_dir' | 40 --amr_matrix_png_dir 'amr_matrix_png_dir' |
41 --errors '$errors' | |
41 #if str($output_process_log) == 'yes': | 42 #if str($output_process_log) == 'yes': |
42 && mv 'process_log' '$process_log' | 43 && mv 'process_log' '$process_log' |
43 #end if | 44 #end if |
44 ]]></command> | 45 ]]></command> |
45 <inputs> | 46 <inputs> |
72 </inputs> | 73 </inputs> |
73 <outputs> | 74 <outputs> |
74 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> | 75 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> |
75 <filter>output_process_log == 'yes'</filter> | 76 <filter>output_process_log == 'yes'</filter> |
76 </data> | 77 </data> |
78 <data name="errors" format="txt" label="${tool.name} on ${on_string} (errors)"/> | |
77 <collection name="mutation_regions_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (mutation regions)"> | 79 <collection name="mutation_regions_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (mutation regions)"> |
78 <filter>amr_mutation_regions_bed_file not in [None, 'None']</filter> | 80 <filter>amr_mutation_regions_bed_file not in [None, 'None']</filter> |
79 <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>tsv)" directory="mutation_regions_dir"/> | 81 <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>tsv)" directory="mutation_regions_dir"/> |
80 </collection> | 82 </collection> |
81 <collection name="amr_matrix_png" type="list" format="png"> | 83 <collection name="amr_matrix_png" type="list" format="png"> |
97 <assert_contents> | 99 <assert_contents> |
98 <has_size value="25383" delta="100"/> | 100 <has_size value="25383" delta="100"/> |
99 </assert_contents> | 101 </assert_contents> |
100 </element> | 102 </element> |
101 </output_collection> | 103 </output_collection> |
104 <output name="errors" value="errors.txt" ftype="txt"/> | |
102 </test> | 105 </test> |
103 </tests> | 106 </tests> |
104 <help> | 107 <help> |
105 **What it does** | 108 **What it does** |
106 | 109 |