Mercurial > repos > greg > draw_amr_matrix
comparison draw_amr_matrix.xml @ 7:389c98d344ce draft
Uploaded
author | greg |
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date | Fri, 03 Mar 2023 22:03:09 +0000 |
parents | 33a0ea992043 |
children | 70073df30a06 |
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6:caf554e039b2 | 7:389c98d344ce |
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6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 #import re | 8 #import re |
9 | 9 |
10 mkdir amr_feature_hits_dir && | 10 mkdir amr_feature_hits_dir && |
11 mkdir mutations_dir && | 11 mkdir mutation_regions_dir && |
12 mkdir output_dir && | 12 mkdir amr_matrix_png_dir && |
13 | 13 |
14 #if $reference_source.reference_source_selector == 'history': | 14 #if $reference_source.reference_source_selector == 'history': |
15 ln -f -s '$reference_source.ref_file' reference.fa && | 15 ln -f -s '$reference_source.ref_file' reference.fa && |
16 #else: | 16 #else: |
17 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && | 17 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && |
26 python '$__tool_directory__/draw_amr_matrix.py' | 26 python '$__tool_directory__/draw_amr_matrix.py' |
27 --amr_feature_hits_dir 'amr_feature_hits_dir' | 27 --amr_feature_hits_dir 'amr_feature_hits_dir' |
28 #if str($amr_deletions_file) != 'None': | 28 #if str($amr_deletions_file) != 'None': |
29 --amr_deletions_file '$amr_deletions_file' | 29 --amr_deletions_file '$amr_deletions_file' |
30 #end if | 30 #end if |
31 #if str($amr_mutations_file) != 'None': | 31 #if str($varscan_vcf_file) != 'None': |
32 --amr_mutations_file '$amr_mutations_file' | 32 --varscan_vcf_file '$varscan_vcf_file' |
33 #end if | 33 #end if |
34 #if str($amr_mutation_regions_file) != 'None': | 34 #if str($amr_mutation_regions_bed_file) != 'None': |
35 --amr_mutation_regions_file '$amr_mutation_regions_file' | 35 --amr_mutation_regions_bed_file '$amr_mutation_regions_bed_file' |
36 --region_mutations_output_file '$region_mutations_output_file' | 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 --mutations_dir 'mutations_dir' | 40 --amr_matrix_png_dir 'amr_matrix_png_dir' |
41 --output_dir 'output_dir' | |
42 #if str($output_process_log) == 'yes': | 41 #if str($output_process_log) == 'yes': |
43 && mv 'process_log' '$process_log' | 42 && mv 'process_log' '$process_log' |
44 #end if | 43 #end if |
45 ]]></command> | 44 ]]></command> |
46 <inputs> | 45 <inputs> |
61 <param name="ref_file" type="data" format="fasta,fastq" label="Select the reference sequence" help="You can upload a FASTA file and use it as reference"/> | 60 <param name="ref_file" type="data" format="fasta,fastq" label="Select the reference sequence" help="You can upload a FASTA file and use it as reference"/> |
62 </when> | 61 </when> |
63 </conditional> | 62 </conditional> |
64 <param argument="--amr_feature_hits" format="bed" type="data_collection" collection_type="list" label="Collection of feature hits BED files"/> | 63 <param argument="--amr_feature_hits" format="bed" type="data_collection" collection_type="list" label="Collection of feature hits BED files"/> |
65 <param argument="--amr_deletions_file" type="data" format="bed" optional="true" label="AMR deletions file" help="Optional, leave blank to ignore"/> | 64 <param argument="--amr_deletions_file" type="data" format="bed" optional="true" label="AMR deletions file" help="Optional, leave blank to ignore"/> |
66 <param argument="--amr_mutations_file" type="data" format="tabular,tsv" optional="true" label="AMR mutations file" help="Optional, leave blank to ignore"/> | 65 <param argument="--varscan_vcf_file" type="data" format="vcf" optional="true" label="Varscan VCF file" help="Optional, leave blank to ignore"/> |
67 <param argument="--amr_mutation_regions_file" type="data" format="bed" optional="true" label="AMR mutation regions BED file" help="Optional, leave blank to ignore"/> | 66 <param argument="--amr_mutation_regions_bed_file" type="data" format="bed" optional="true" label="AMR mutation regions BED file" help="Optional, leave blank to ignore"/> |
68 <param argument="--amr_gene_drug_file" type="data" format="tabular,tsv" label="AMR gene drugs file"/> | 67 <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?"> | 68 <param name="output_process_log" type="select" display="radio" label="Output process log file?"> |
70 <option value="no" selected="true">No</option> | 69 <option value="no" selected="true">No</option> |
71 <option value="yes">Yes</option> | 70 <option value="yes">Yes</option> |
72 </param> | 71 </param> |
73 </inputs> | 72 </inputs> |
74 <outputs> | 73 <outputs> |
75 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> | 74 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)"> |
76 <filter>output_process_log == 'yes'</filter> | 75 <filter>output_process_log == 'yes'</filter> |
77 </data> | 76 </data> |
78 <data name="region_mutations_output_file" format="tsv" label="${tool.name} on ${on_string} (region mutations)"> | 77 <collection name="mutation_regions_tsv" type="list" format="tsv" label="${tool.name} on ${on_string} (mutation regions)"> |
79 <filter>amr_mutation_regions_file not in [None, 'None']</filter> | 78 <filter>amr_mutation_regions_bed_file not in [None, 'None']</filter> |
80 </data> | 79 <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>tsv)" directory="mutation_regions_dir"/> |
80 </collection> | |
81 <collection name="amr_matrix_png" type="list" format="png"> | 81 <collection name="amr_matrix_png" type="list" format="png"> |
82 <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>png)" directory="output_dir"/> | 82 <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>png)" directory="amr_matrix_png_dir"/> |
83 </collection> | 83 </collection> |
84 </outputs> | 84 </outputs> |
85 <tests> | 85 <tests> |
86 <test> | 86 <test> |
87 <param name="reference_source_selector" value="history"/> | 87 <param name="reference_source_selector" value="history"/> |