view bcbio-nextgen.xml @ 0:2ed60a09d6b6 draft

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<tool id="bcbio-nextgen" name="BCBio" version="0.1.0">
    <command detect_errors="exit_code"><![CDATA[
        PATH="/home/bioinf/bcbio_test/tool_dir/bin:/home/bioinf/bcbio_test/anaconda/bin:\$PATH" && 
        mkdir $everything_else.files_path && 
        cd $everything_else.files_path &&
        python $__tool_directory__/script.py --workdir `pwd` --output-dir `pwd`/output --template $main --output-conf `pwd`/config.yaml
        #if str( $region_file.has_region_file_select ) == "yes":
          --bed ${region_file.bed} 
        #end if
        #for $i, $sample in enumerate( $samples )
            --input $sample.forward:$sample.reverse:$sample.phenotype
        #end for
        && bcbio_nextgen.py /home/bioinf/bcbio_test/galaxy/bcbio_system.yaml `pwd`/config.yaml && 
        zcat final/*/Batch1-ensemble-annotated.vcf.gz > $output_vcf &&
        python $__tool_directory__/make_html.py --input-dir $everything_else.files_path --root-html $everything_else
    ]]></command>
    <configfiles>
        <configfile name='main'>
details:
{% for sample in samples -%}
- algorithm:
    aligner: $aligner
    mark_duplicates: ${mark_duplicates}
    remove_lcr: ${remove_lcr}
    variantcaller: [$variantcallers]
    {% if bed_file_path -%}  variant_regions: {{ bed_file_path }}{% endif %}
    ensemble:
      numpass: 2
    align_split_size: false
  analysis: $analysis
  lane: {{ loop.index }}
  description: {{ sample['description'] }}
  files: [{{ sample['forward'] }}, {{ sample['reverse'] }}]
  genome_build: $build
  metadata:
    phenotype: {{ sample['phenotype'] }}
    batch: Batch1
  upload:
    dir: ./final
{% endfor %}
        </configfile>
    </configfiles>
    <inputs>
        <param name="build" type="select" label="Genome Build">
            <option value="GRCh37">GRCh37</option>
            <option value="hg19">hg19</option>
            <option value="GRCm38">GRCm38</option>
            <option value="mm10">mm10</option>
        </param>
        <param name="analysis" type="select" label="Analysis">
            <option value="variant2">variant2</option>
            <option value="RNA-seq">RNA-seq</option>
            <option value="smallRNA-seq">smallRNA-seq</option>
        </param>
        <param name="aligner" type="select" label="Aligner">
            <option value="bwa">bwa</option>
            <option value="bowtie">bowtie</option>
            <option value="bowtie2">bowtie2</option>
            <option value="hisat2">hisat2</option>
            <option value="minimap2">minimap2</option>
            <option value="novoalign">novoalign</option>
            <option value="snap">snap</option>
            <option value="star">star</option>
            <option value="tophat2">tophat2</option>
            <option value="false">false</option>
        </param>
        <param name="variantcallers" type="select" multiple="true" label="Variantcallers">
            <option value="false">false</option>
            <option value="freebayes">freebayes</option>
            <option value="gatk-haplotype">gatk-haplotype</option>
            <option value="haplotyper">haplotyper</option>
            <option value="platypus">platypus</option>
            <!--<option value="mutect">mutect</option>-->
            <option value="mutect2">mutect2</option>
            <option value="scalpel">scalpel</option>
            <option value="tnhaplotyper">tnhaplotyper</option>
            <option value="tnscope">tnscope</option>
            <option value="vardict">vardict</option>
            <option value="varscan">varscan</option>
            <option value="samtools">samtools</option>
            <option value="gatk">gatk</option>
        </param>
        <param name="mark_duplicates" type="select">
            <option value="true" selected="true">true</option>
            <option value="false">false</option>
        </param>
        <param name="remove_lcr" type="select">
            <option value="true" selected="true">true</option>
            <option value="false">false</option>
        </param>
        <repeat name="samples" title="Samples" min="1">
            <param name="phenotype" type="select" label="Phenotype">
                <option value="normal">Normal</option>
                <option value="tumor">Tumor</option>
            </param>
            <param type="data" name="forward" format="fastq,fastq.gz,fastqsanger.gz" />
            <param type="data" name="reverse" format="fastq,fastq.gz,fastqsanger.gz" />
        </repeat>
        <conditional name="region_file">
            <param name="has_region_file_select" type="select" label="Do you have a region file">
                <option value="yes">Yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <param type="data" name="bed" format="bed" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_vcf" format="vcf"/>
        <data name="everything_else" format="html"/>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>