Mercurial > repos > greg > draw_amr_matrix

comparison draw_amr_matrix.xml @ 9:70073df30a06 draft

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Uploaded
author greg
date Tue, 21 Mar 2023 14:06:11 +0000
parents 389c98d344ce
children da1c9c1be421
comparison
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8:7fe8ea50a81d 9:70073df30a06
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&lt;designation&gt;.+)\.(?P&lt;ext&gt;tsv)" directory="mutation_regions_dir"/> 81 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;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