comparison hydra.xml @ 4:8cdffc02d2e2 draft

planemo upload for repository https://github.com/phac-nml/quasitools commit 19e0f266ee455b82432e2d7b987b35de8c7a14d5

3:8dacd75ca8f1

<tool id="hydra" name="Hydra pipeline" version="0.1.0">
    <description>Identifies drug resistance within an NGS dataset</description>
    <requirements>
          <requirement type="package" version="0.2.3">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        quasitools hydra 

        #if $min_freq:
            -mf '$min_freq' 
        #end if

        #if $generate_consensus:
            --generate_consensus 
        #end if

        #if $filter_ns:
            --ns 
        #end if

        <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021."/>
        <param name="min_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for variant to be considered later on in the pipeline. Defaults to 30." />
        <param name="min_depth" type="integer" optional="true" min="0" max="5000" label="Minimum depth" value="100" help="Minimum required depth for variant to be considered later on in the pipeline. Defaults to 100." />
        <param name="min_ac" type="integer" optional="true" min="0" max="5000" label="Minimum allele count" value="5" help="Minimum required allele count for variant to be considered later on in the pipeline. Defaults to 5." />
        <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="Minimum required frequency for variant to be considered later on in the pipeline. Defaults to 0.01." />
        <param name="generate_consensus" type="boolean" truevalue="--generate_consensus" falsevalue="" checked="False" label="Generate consensus" />
        <param name="filter_ns" type="boolean" truevalue="--ns" falsevalue="" checked="False" label="Filter out n's" />
    </inputs>
    <outputs>
        <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" />
        <data format="bam" label="HyDRA: bam.bai output" name="output_bam_bai" from_work_dir="output/align.bam.bai" />

        <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" />
        <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" />
        <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" />
        <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" />
        <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" />
        <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta">
            <filter>generate_consensus</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="type" value="single"/>

4:8cdffc02d2e2

<tool id="hydra" name="Hydra pipeline" version="0.2.0">
    <description>Identifies drug resistance within an NGS dataset</description>
    <requirements>
          <requirement type="package" version="0.3.1">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        quasitools hydra 

        #if $min_freq:
            -mf '$min_freq' 
        #end if

        #if $consensus.consensus_bool == "true_consensus":
            --generate_consensus 

            #if $consensus.fasta_id.type == "default":
                --id 
                #if $data_type.type == "paired":
                    '${fastq_input1.element_identifier}'_'${fastq_input2.element_identifier}'
                #elif $data_type.type == "single":
                    '${fastq_input1.element_identifier}'
                #end if
            #elif $consensus.fasta_id.type == "custom":
                --id '$consensus.fasta_id.custom_id' 
            #end if
        #end if

        #if $filter_ns:
            --ns 
        #end if

        <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021."/>
        <param name="min_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for variant to be considered later on in the pipeline. Defaults to 30." />
        <param name="min_depth" type="integer" optional="true" min="0" max="5000" label="Minimum depth" value="100" help="Minimum required depth for variant to be considered later on in the pipeline. Defaults to 100." />
        <param name="min_ac" type="integer" optional="true" min="0" max="5000" label="Minimum allele count" value="5" help="Minimum required allele count for variant to be considered later on in the pipeline. Defaults to 5." />
        <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="Minimum required frequency for variant to be considered later on in the pipeline. Defaults to 0.01." />
        <conditional name="consensus">
            <param name="consensus_bool" type="select" label="Generate consensus sequence." multiple="false" display="radio">
                <option value="true_consensus">True</option>
                <option selected="true" value="false_consensus">False</option>
            </param>
            <when value="true_consensus"> 
                <conditional name="fasta_id">
                    <param name="type" type="select" label="Specify consensus fasta identifier" multiple="false" display="radio">
                        <option value="default" >Use fasta dataset name</option>
                        <option value="custom">Use custom name</option>
                    </param>
                    <when value="default">
                    </when>
                    <when value="custom">
                        <param name="custom_id" type="text" optional="false" value="custom_id" label="Fasta identifier" help="Type in a fasta identifier."/>
                    </when>
                </conditional>            
            </when>
            <when value="false_consensus"> 
            </when>
        </conditional>
        <param name="filter_ns" type="boolean" truevalue="--ns" falsevalue="" checked="False" label="Filter out n's" />
    </inputs>
    <outputs>
        <data format="bam" label="HyDRA: alignment bam output" name="output_bam" from_work_dir="output/align.bam" />
        <data format="bam" label="HyDRA: bam.bai output" name="output_bam_bai" from_work_dir="output/align.bam.bai" />

        <data format="csv" label="HyDRA: drug resistance output" name="output_dr" from_work_dir="output/dr_report.csv" />
        <data format="fastq" label="HyDRA: filtered reads output" name="output_filtered" from_work_dir="output/filtered.fastq" />
        <data format="vcf" label="HyDRA: variants output" name="output_hydra" from_work_dir="output/hydra.vcf" />
        <data format="vcf" label="HyDRA: aa mutations output" name="output_aa_mt" from_work_dir="output/mutation_report.hmcf" />
        <data format="txt" label="HyDRA: stats output" name="output_stats" from_work_dir="output/stats.txt" />
        <data format="fasta" label="HyDRA: consensus output" name="output_consensus" from_work_dir="output/consensus.fasta" >
            <filter>consensus['consensus_bool'] == "true_consensus"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="type" value="single"/>