comparison tb_profiler_profile.xml @ 3:19793eecc9f0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"

2:49b819f88c2b

<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.4">
    <description>Infer strain types and drug resistance markers from sequences</description>
    <requirements>
        <requirement type="package" version="2.4">tb-profiler</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
            #if str($fastq_or_bam.input_select.value) == "paired_fastq"
                #set r1_ext = $fastq_or_bam.read1.extension

        #if $advanced.options == 'yes'
            --call_method '${advanced.call_method}'
            --min_gene_frac '${advanced.min_gene_frac}'
            --mapper '${advanced.mapper}'
            --min_depth '${advanced.min_depth}'
        #end if

        #if $output_format == "pdf"
            --pdf
        #else if $output_format == "txt"

                    <option value="bwa" selected="true">bwa</option>
                    <option value="minimap2">minimap2</option>
                    <option value="bowtie2">bowtie2</option>
                </param>
                <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>

3:19793eecc9f0

<tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0">
    <description>Infer strain types and drug resistance markers from sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
            #if str($fastq_or_bam.input_select.value) == "paired_fastq"
                #set r1_ext = $fastq_or_bam.read1.extension

        #if $advanced.options == 'yes'
            --call_method '${advanced.call_method}'
            --min_gene_frac '${advanced.min_gene_frac}'
            --mapper '${advanced.mapper}'
            --min_depth '${advanced.min_depth}'
            --af '${min_allel_freq}'
            --reporting_af '${min_allel_freq_reporting}'
        #end if

        #if $output_format == "pdf"
            --pdf
        #else if $output_format == "txt"

                    <option value="bwa" selected="true">bwa</option>
                    <option value="minimap2">minimap2</option>
                    <option value="bowtie2">bowtie2</option>
                </param>
                <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)" />
                <param name="min_allel_freq" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants" help=" Minimum allele frequency to call variants (default: 0.1)" />
                <param name="min_allel_freq_reporting" argument="--reporting_af" value="0.1" label="Reporting Minimum allele frequency to call variants" type="float" help=" Minimum allele frequency to call variants (default: 0.1)"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>