comparison pima_report.xml @ 14:95b1d1a9497d draft

Uploaded

13:f03c80bb22e9

    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#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($bedtools_complementbed_file) not in ['None', '']:
    #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier))
#end if

#if str($flye_assembly_info_file) not in ['None', '']:
    --flye_assembly_info_file '$flye_assembly_info_file'
    --flye_version '$flye_version'
#end if
--genome_insertions_file '$genome_insertions_file'
#if $illumina_fastq_file.ext.endswith(".gz"):
    --gzipped
#end if
--illumina_fastq_file '$illumina_fastq_file'
#if str($kraken2_report_file) not in ['None', '']:
    --kraken2_report_file '$kraken2_report_file'
    --kraken2_version '$kraken2_version'
#end if
#if str($minimap2_bam_file) not in ['None', '']:

        <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"/>
        <param name="flye_assembly_info_file" type="data" format="tabular,tsv" optional="true" label="Flye assembly info tabular file" help="Optional, ignored if not selected"/>
        <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
        <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
        <param name="illumina_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="Fastq sample file"/>
        <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
        <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
        <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
        <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
        <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>

    <tests>
        <test>
            <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
            <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
            <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
            <param name="illumina_fastq_file" value="illumina_fastq.fastq" ftype="fastq"/>
            <output name="output" value="output.pdf" ftype="pdf"/>
        </test>
    </tests>
    <help>
**What it does**

14:95b1d1a9497d

    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import re

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

#if str($bedtools_complementbed_file) not in ['None', '']:
    #set bedtools_version = re.sub('[^\s\w\-]', '_', str($bedtools_complementbed_file.element_identifier))
#end if

#if str($flye_assembly_info_file) not in ['None', '']:
    --flye_assembly_info_file '$flye_assembly_info_file'
    --flye_version '$flye_version'
#end if
--genome_insertions_file '$genome_insertions_file'
#if $ont_fastq_file.ext.endswith(".gz"):
    --gzipped
#end if
--ont_fastq_file '$ont_fastq_file'
#if str($kraken2_report_file) not in ['None', '']:
    --kraken2_report_file '$kraken2_report_file'
    --kraken2_version '$kraken2_version'
#end if
#if str($minimap2_bam_file) not in ['None', '']:

        <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"/>
        <param name="flye_assembly_info_file" type="data" format="tabular,tsv" optional="true" label="Flye assembly info tabular file" help="Optional, ignored if not selected"/>
        <param name="genome_insertions_file" type="data" format="bed" label="Genome insertions BED file"/>
        <param name="kraken2_report_file" type="data" format="tabular,tsv" optional="true" label="Kraken2 report tabular file" help="Optional, ignored if not selected"/>
        <param name="ont_fastq_file" type="data" format="fastqsanger,fastqsanger.gz" label="ONT fastq sample file"/>
        <param name="minimap2_bam_file" type="data" format="bam" label="Minimap2 BAM file"/>
        <param name="mutation_regions" format="tabular,tsv" type="data_collection" collection_type="list" label="Collection of mutation regions tabular files"/>
        <param name="mutation_regions_bed_file" type="data" format="mutations_regions,bed" label="Mutation regions BED file"/>
        <param name="quast_report_file" type="data" format="tabular" label="Quast report tabular file"/>
        <param name="reference_insertions_file" type="data" format="bed" label="Reference insertions BED file"/>

    <tests>
        <test>
            <param name="aligned_sample" value="aligned_sample.bam" ftype="bam"/>
            <param name="assembly_fasta_file" value="assembly_fasta.fasta" ftype="fasta"/>
            <param name="contig_coverage_file" value="contig_coverage.tabular" ftype="tabular"/>
            <param name="ont_fastq_file" value="ont_fastq.fastq" ftype="fastq"/>
            <output name="output" value="output.pdf" ftype="pdf"/>
        </test>
    </tests>
    <help>
**What it does**