Mercurial > repos > greg > draw_amr_matrix
comparison draw_amr_matrix.xml @ 15:487a3c008812 draft
Uploaded
author | greg |
---|---|
date | Mon, 01 May 2023 17:52:05 +0000 |
parents | c5e80637cf3d |
children |
comparison
equal
deleted
inserted
replaced
14:c5e80637cf3d | 15:487a3c008812 |
---|---|
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 '$errors' | 41 --errors '$errors' |
42 --in_test_mode '$in_test_mode' | |
43 #if str($output_process_log) == 'yes': | 42 #if str($output_process_log) == 'yes': |
44 && mv 'process_log' '$process_log' | 43 && mv 'process_log' '$process_log' |
45 #end if | 44 #end if |
46 ]]></command> | 45 ]]></command> |
47 <inputs> | 46 <inputs> |
69 <param argument="--amr_gene_drug_file" type="data" format="tabular,tsv" label="AMR gene drugs file"/> | 68 <param argument="--amr_gene_drug_file" type="data" format="tabular,tsv" label="AMR gene drugs file"/> |
70 <param name="output_process_log" type="select" display="radio" label="Output process log file?"> | 69 <param name="output_process_log" type="select" display="radio" label="Output process log file?"> |
71 <option value="no" selected="true">No</option> | 70 <option value="no" selected="true">No</option> |
72 <option value="yes">Yes</option> | 71 <option value="yes">Yes</option> |
73 </param> | 72 </param> |
74 <param name="in_test_mode" type="hidden" value="false"/> | |
75 </inputs> | 73 </inputs> |
76 <outputs> | 74 <outputs> |
77 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> | 75 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> |
78 <filter>output_process_log == 'yes'</filter> | 76 <filter>output_process_log == 'yes'</filter> |
79 </data> | 77 </data> |
96 </collection> | 94 </collection> |
97 </param> | 95 </param> |
98 <param name="varscan_vcf_file" value="varscan.vcf" ftype="vcf"/> | 96 <param name="varscan_vcf_file" value="varscan.vcf" ftype="vcf"/> |
99 <param name="amr_mutation_regions_bed_file" value="amr_mutation_regions.bed" ftype="bed"/> | 97 <param name="amr_mutation_regions_bed_file" value="amr_mutation_regions.bed" ftype="bed"/> |
100 <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/> | 98 <param name="amr_gene_drug_file" value="amr_gene_drug.tsv" ftype="tsv"/> |
101 <param name="in_test_mode" value="true"/> | |
102 <output_collection name="amr_matrix_png" type="list" count="1"> | 99 <output_collection name="amr_matrix_png" type="list" count="1"> |
103 <element name="amr_matrix" ftype="png"> | 100 <element name="amr_matrix" ftype="png"> |
104 <assert_contents> | 101 <assert_contents> |
105 <has_size value="28798" delta="1000"/> | 102 <has_size value="28798" delta="1000"/> |
106 </assert_contents> | 103 </assert_contents> |