Mercurial > repos > greg > pima_report

comparison pima_report.xml @ 25:4986a7fb2145 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 20 Apr 2023 18:47:01 +0000
parents d89b7d47a85a
children 46edd7435555
comparison
equal deleted inserted replaced
24:803e5965ed20 25:4986a7fb2145
5 </macros> 5 </macros>
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 #set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier)) 10 #if str($read_type) == 'ont':
11 #set analysis_name = re.sub('[^\s\w\-]', '_', str($fastq_file.element_identifier))
12 #else:
13 #set analysis_name = re.sub('[^\s\w\-]', '_', str($extracted_fastq_file.element_identifier))
14 #end if
11 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier)) 15 #set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))
12 16
13 #if str($bedtools_complementbed_file) not in ['None', '']: 17 #if str($bedtools_complementbed_file) not in ['None', '']:
14 #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier)) 18 #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier))
15 #end if 19 #end if
135 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/> 139 <param name="circos_png" format="png" type="data_collection" collection_type="list" label="Collection of circos PNG files"/>
136 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/> 140 <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
137 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/> 141 <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
138 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/> 142 <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
139 <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/> 143 <param name="errors_file" type="data" format="txt" label="AMR mutation regions error txt file"/>
144 <param name="extracted_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" optional="true" label="Fastq sample file extracted from a paired collection" help="Used only with Illumina paired reads, leave blank to ignore"/>
140 <param name="fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/> 145 <param name="fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
141 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/> 146 <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
142 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/> 147 <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>
143 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/> 148 <param name="assembler_version_file" type="data" format="fasta,tabular,tsv" optional="true" label="Assembly version file" help="Optional, ignored if not selected"/>
144 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/> 149 <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>