Mercurial > repos > bgruening > hicup_hicup
view hicup_hicup.xml @ 4:bd1594d55a38 draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author | bgruening |
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date | Fri, 25 May 2018 17:53:14 -0400 |
parents | e96cb39c3f8e |
children | 6137fb382a02 |
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<tool id="hicup_hicup" name="Hicup Pipeline" version="@VERSION@.0"> <description>controls the other programs in the HiCUP pipeline.</description> <macros> <import>hicup_macros.xml</import> </macros> <expand macro="requirements_hicup" /> <command detect_errors="exit_code"><![CDATA[ ##Dealing with fastq and fastq.gz #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): ln -s $input_first_sequence dataset1.gz && #set input1='dataset1.gz' #else ln -s $input_first_sequence dataset1 && #set input1='dataset1' #end if #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): ln -s $input_second_sequence dataset2.gz && #set input2='dataset2.gz' #else ln -s $input_second_sequence dataset2 && #set input2='dataset2' #end if BOWTIE_PATH_BASH="\$(which bowtie2)" && #set index_path = '' #if str($reference_genome.source) == "history": bowtie2-build "$reference_genome.own_file" genome && ln -s "$reference_genome.own_file" genome.fa && #set index_path = 'genome' #else: #set index_path = $reference_genome.index.fields.path #end if hicup_digester --re1 '$re1' --genome '$genome' #if $advanced_options.re2: --re2 '$advanced_options.re2' #end if #for $file in $input_files_digest: $file #end for && mv *Digest_* digest_file.txt && hicup --zip --threads \${GALAXY_SLOTS:-1} --digest digest_file.txt --index '$index_path' --bowtie2 \$BOWTIE_PATH_BASH $advanced_options.nofill --keep #if $advanced_options.longest: --longest '$advanced_options.longest' #end if #if $advanced_options.shortest: --shortest '$advanced_options.shortest' #end if $input1 $input2 && ls -al ]]></command> <inputs> <expand macro="input_files" /> <param name="input_files_digest" type="data" multiple="true" format="fasta" label="Input DNA sequence files that should be digested"/> <param argument="--genome" type="text" label="Genome name" help="Name of the genome to be digested."/> <expand macro="re1" /> <expand macro="reference_genome_macro" /> <section name="advanced_options" title="Advanced options"> <expand macro="re2" /> <expand macro="filter_longest_shortest" /> <expand macro="no_fill" /> </section> </inputs> <outputs> <!-- Regular output of hicup --> <data name="hicup_results" format="html" from_work_dir="*.html" label="HiCUP results"/> <data name="hicup_report" format="txt" from_work_dir="HiCUP_summary_report*.txt" label="HiCUP report" /> <data name="dataset_hicup" format="qname_sorted.bam" from_work_dir="*.hicup.*bam" label="HiCUP data result"/> <collection name="intermediate_results" label="HiCUP intermediate results" type="list"> <!-- Output of the truncater step --> <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt" /> <data name="dataset1_trunc" format="fastq.gz" label="Hicup Dataset1 Truncation" from_work_dir="dataset1*.trunc.fastq.gz" /> <data name="dataset2_trunc" format="fastq.gz" label="Hicup Dataset2 Truncation" from_work_dir="dataset2*.trunc.fastq.gz" /> <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1*.truncation_barchart.svg" /> <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2*.truncation_barchart.svg" /> <!-- Output of the mapper step --> <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary*" label="hicup_mapper_summary.txt"/> <data name="result_pair" format="qname_sorted.bam" from_work_dir="*pair.bam" label="pair.bam"/> <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1*.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" /> <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2*.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" /> <!-- Output of the filter step --> <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" /> <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" /> <data name="contiguous_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*contiguous.filter.bam" label="contiguous.filter.bam" /> <data name="re_ligation_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*re_ligation.filter.bam" label="re_ligation.filter.bam" /> <data name="same_dangling_ends_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_dangling_ends.filter.bam" label="same_dangling_ends.filter.bam" /> <data name="invalid_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*invalid.filter.bam" label="invalid.filter.bam" /> <data name="same_circularised_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_circularised.filter.bam" label="same_circularised.filter.bam" /> <data name="same_internal_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_internal.filter.bam" label="same_internal.filter.bam" /> <data name="wrong_size_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*wrong_size.filter.bam" label="wrong_size.filter.bam"/> <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" /> <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> <!-- Output of the deduplicator step --> <data name="cis_trans_piechart" format="svg" from_work_dir="*deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/> <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" /> <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" /> </collection> </outputs> <tests> <test> <!-- inputs --> <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/> <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/> <param name="re1" value="A^AGCTT"/> <param name="input_files_digest" value="chr21And22FromHg38.fasta"/> <param name="genome" value="chr21And22FromHg38"/> <conditional name="reference_genome"> <param name="source" value="history" /> <param name="own_file" value="chr21And22FromHg38.fasta"/> </conditional> <!-- outputs --> <output name="hicup_results" file="HiCUP_summary_report.html" ftype="html" lines_diff="10000"/> <output name="dataset_hicup" file="dataset1_2.hicup.bam" lines_diff="10" ftype="qname_sorted.bam" /> <output name="hicup_report" file="HiCUP_summary_report.txt" lines_diff="2"/> <output_collection name="intermediate_results"> <!-- truncater step--> <element name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/> <element name="dataset1_trunc" file="dataset1.trunc.fastq.gz" compare="sim_size"/> <element name="dataset2_trunc" file="dataset2.trunc.fastq.gz" compare="sim_size"/> <element name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" /> <element name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" /> <!-- mapper step --> <element name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/> <element name="result_pair" file="dataset1_2.pair.bam" lines_diff="8" ftype="qname_sorted.bam"/> <element name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> <element name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> <!-- filter step--> <element name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> <element name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="8" ftype="qname_sorted.bam" /> <element name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> <element name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> <element name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> <element name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> <element name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> <element name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> <element name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" lines_diff="1000" /> <element name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" lines_diff="1000" /> <!-- deduplicator step--> <element name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/> <element name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/> <element name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/> </output_collection> </test> </tests> <help><![CDATA[ For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ To get more information about the pipeline visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#HiCUP ]]></help> <expand macro="citation_hicup" /> </tool>