Mercurial > repos > greg > draw_amr_matrix

comparison draw_amr_matrix.xml @ 7:389c98d344ce draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 03 Mar 2023 22:03:09 +0000
parents 33a0ea992043
children 70073df30a06
comparison
equal deleted inserted replaced
6:caf554e039b2 7:389c98d344ce
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&lt;designation&gt;.+)\.(?P&lt;ext&gt;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&lt;designation&gt;.+)\.(?P&lt;ext&gt;png)" directory="output_dir"/> 82 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.(?P&lt;ext&gt;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"/>