comparison pima_report.xml @ 3:33d9832420c5 draft

Uploaded

2:9cb62054a87a

#import re

#set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
#set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))

#if str($blastn_file) not in ['None', '']:
    #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_file.element_identifier))
#end if
#set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
#set dnadiff_version = $dnadiff_version.rstrip('(snps)')
#if str($flye_assembly_info_file) not in ['None', '']:
    #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
    #set flye_version = $flye_version.rstrip('(assembly info)')

    <inputs>
        <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/>
        <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
        <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
        <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
        <param name="blastn_file" type="data" format="bam" label="Blastn BAM file"/>
        <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
        <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
        <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
        <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
        <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>

3:33d9832420c5

#import re

#set analysis_name = re.sub('[^\s\w\-]', '_', str($illumina_fastq_file.element_identifier))
#set assembly_name = re.sub('[^\s\w\-]', '_', str($assembly_fasta_file.element_identifier))

#set blastn_version = 'unknown'
#for $i in $blastn_features:
    #set blastn_version = re.sub('[^\s\w\-]', '_', str($blastn_file.element_identifier))
#end for

#set dnadiff_version = re.sub('[^\s\w\-]', '_', str($dnadiff_snps_file.element_identifier))
#set dnadiff_version = $dnadiff_version.rstrip('(snps)')
#if str($flye_assembly_info_file) not in ['None', '']:
    #set flye_version = re.sub('[^\s\w\-]', '_', str($flye_assembly_info_file.element_identifier))
    #set flye_version = $flye_version.rstrip('(assembly info)')

    <inputs>
        <param name="amr_matrices_png" format="png" type="data_collection" collection_type="list" label="Collection of AMR matrix PNG files"/>
        <param name="aligned_sample" type="data" format="bam" label="Aligned sample BAM file"/>
        <param name="amr_deletions_file" type="data" format="bed" label="AMR deletions BED file"/>
        <param name="assembly_fasta_file" type="data" format="fasta" label="Assembly FASTA file"/>
        <param name="blastn_features" format="bam" type="data_collection" collection_type="list" label="Collection of blastn BAM files"/>
        <param name="compute_sequence_length_file" type="data" format="tabular,tsv" label="Compute sequence length tabular file"/>
        <param name="contig_coverage_file" type="data" format="tabular,tsv" label="Contig coverage tabular file"/>
        <param name="dnadiff_snps_file" type="data" format="tabular" label="DNAdiff snps tabular file"/>
        <param name="features_bed" format="bed" type="data_collection" collection_type="list" label="Collection of best feature hits BED files"/>
        <param name="features_png" format="png" type="data_collection" collection_type="list" label="Collection of best feature hits PNG files"/>