Mercurial > repos > bgruening > hicup2juicer
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 50173a1994a72d9774fd46777de94dd02d35bd42
author | bgruening |
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date | Mon, 24 Oct 2022 16:09:44 +0000 |
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children | b4e7244246e2 |
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<tool id="hicup2juicer" name="Hicup to juicer converter" version="@VERSION@+galaxy0"> <description></description> <macros> <import>hicup_macros.xml</import> </macros> <expand macro="requirements_hicup" /> <command detect_errors="exit_code"><![CDATA[ #if $input_file.ext != 'sam': #set ext='bam' #else: #set ext='sam' #end if ln -s '$input_file' input.$ext && hicup2juicer input.$ext ]]> </command> <inputs> <param name="input_file" type="data" format="qname_sorted.bam,sam" label="Output of HiCUP to convert" /> </inputs> <outputs> <data name="output" format="tabular" label="${tool.name} on ${on_string}: Pairs in juicebox format" from_work_dir="*.prejuicer" /> </outputs> <tests> <test expect_num_outputs="1"> <param name="input_file" value="dataset1_2.hicup.bam"/> <output name="output" value="dataset1_2.hicup.bam.prejuicer"/> </test> </tests> <help><![CDATA[ HiCUP homepage: www.bioinformatics.babraham.ac.uk/projects/hicup The hicup2juicer script converts HiCUP BAM/SAM files to a format compatible with Juicer and JuiceBox( https://github.com/aidenlab/juicer ). Outputfiles generated by this script may be converted to Juicer ".hic" files using the "pre" command as described at: https://github.com/aidenlab/juicer/wiki/Pre The script does not use restriction site coordinates when generating output. FUNCTION HiCUP generates SAM/BAM files of mapped, filtered paired-end reads constituting the sequenced valid Hi-C di-tags. These may then be analysed by a variety of specialised tools, but before this is possible the datasets will need parsing into an appropriate format. The hicup2juicer script converts HiCUP BAM/SAM files to a tab-delimited format comprising 7 columns, with read pairs on the same line: <readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2> str = strand (0 for forward, anything else for reverse) chr = chromosome (must be a chromosome in the genome) pos = position frag = restriction site fragment mapq = mapping quality score Column1: Readpair index number (starting at 1) Column2: forward read strand (0 = positive strand, 1 = negative strand) Column3: forward read chromosome name Column4: forward read position Column5: forward read fragment id (set to the dummy value 0) Column6: reverse read strand (0 = positive strand, 1 = negative strand) Column7: reverse read chromosome name Column8: reverse read position Column9: reverse read fragment id (set to the dummy value 1) Column10: forward read MAPQ score Column11: reverse read MAPQ score COMMAND LINE OPTIONS --help Print help message and exit --version Print the program version and exit --zip Write output to a gzip file Full instructions on running the pipeline can be found at: www.bioinformatics.babraham.ac.uk/projects/hicup Steven Wingett, Babraham Institute, Cambridge, UK ]]> </help> <expand macro="citation_hicup" /> </tool>