comparison pima_report.xml @ 3:33d9832420c5 draft

Uploaded
author greg
date Thu, 09 Mar 2023 16:44:59 +0000
parents 9cb62054a87a
children 428aed51c487
comparison
equal deleted inserted replaced
2:9cb62054a87a 3:33d9832420c5
8 #import re 8 #import re
9 9
10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier)) 10 #set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier)) 11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
12 12
13 #if str($blastn_file) not in ['None', '']: 13 #set blastn_version = 'unknown'
14 #for $i in $blastn_features:
14 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_file.element_identifier)) 15 #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_file.element_identifier))
15 #end if 16 #end for
17
16 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier)) 18 #set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
17 #set dnadiff_version = $dnadiff_version.rstrip('(snps)') 19 #set dnadiff_version = $dnadiff_version.rstrip('(snps)')
18 #if str($flye_assembly_info_file) not in ['None', '']: 20 #if str($flye_assembly_info_file) not in ['None', '']:
19 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier)) 21 #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
20 #set flye_version = $flye_version.rstrip('(assembly info)') 22 #set flye_version = $flye_version.rstrip('(assembly info)')
90 <inputs> 92 <inputs>
91 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/> 93 <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/>
92 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/> 94 <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
93 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/> 95 <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
94 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/> 96 <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
95 <param name="blastn_file" type="data" format="bam" label="Blastn BAM file"/> 97 <param name="blastn_features" format="bam" type="data_collection" collection_type="list" label="Collection of blastn BAM files"/>
96 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/> 98 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
97 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> 99 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
98 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/> 100 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
99 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 101 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
100 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> 102 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>