Mercurial > repos > dvanzessen > bcbio_nextgen_emc
view bcbio-nextgen.xml @ 5:00c95e2d8820 draft
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author | dvanzessen |
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date | Mon, 29 Jul 2019 04:17:41 -0400 |
parents | 7211d3a78fe0 |
children | 7d5b46d41ff0 |
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<tool id="bcbio-nextgen" name="BCBio" version="1.0"> <command detect_errors="exit_code"><![CDATA[ PATH="\$BCBIO_DIRECTORY/tool_dir/bin:\$BCBIO_DIRECTORY/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 \$BCBIO_DIRECTORY/galaxy/bcbio_system.yaml `pwd`/config.yaml -t local -n \$BCBIO_CORES && 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>