Mercurial > repos > bgruening > hicexplorer_hicbuildmatrixmicroc
diff hicBuildMatrixMicroC.xml @ 0:0c22e9361298 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 63179f3d35e5dec09cdd01c07c6a4e8af3da777d
| author | bgruening |
|---|---|
| date | Thu, 05 Dec 2024 21:42:17 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicBuildMatrixMicroC.xml Thu Dec 05 21:42:17 2024 +0000 @@ -0,0 +1,223 @@ +<tool id="hicexplorer_hicbuildmatrixmicroc" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>create a contact matrix</description> + <macros> + <token name="@BINARY@">hicBuildMatrixMicroC</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + + mkdir ./QCfolder && + mkdir '$qc.files_path' && + @BINARY@ + --samFiles + #for $repeat in $samFiles: + '${repeat.samFile}' + #end for + + #if $maxLibraryInsertSize: + --maxLibraryInsertSize $maxLibraryInsertSize + #end if + + #if $binSizes: + --binSize + #for $repeat in $binSizes + '${repeat.binSize}' + #end for + #end if + + #if $chromosomeSizes: + --chromosomeSizes '$chromosomeSizes' + #end if + #if $dbKey: + --genomeAssembly '$dbKey' + #else + --genomeAssembly '$samFiles[0].samFile.metadata.dbkey' + #end if + + #if $region: + --region '$region' + #end if + + --outFileName 'matrix.$outputFormat' + + #if $outBam: + $outBam ./unsorted.bam + #end if + + $keepSelfCircles + $skipDuplicationCheck + + #if $minMappingQuality and $minMappingQuality is not None: + --minMappingQuality $minMappingQuality + #end if + + --threads @THREADS@ + + --QCfolder ./QCfolder + && + mv ./QCfolder/* $qc.files_path/ + && + mv '$qc.files_path/hicQC.html' '$qc' + && mv "$qc.files_path"/*.log raw_qc + && mv matrix.$outputFormat matrix + #if $outBam: + && samtools sort -@ @THREADS@ -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam + #end if +]]> + </command> + <inputs> + <!-- can we use multiple=True here with min="2" and max="2" ? --> + <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file."> + <param name="samFile" type="data" format="sam,qname_input_sorted.bam"> + </param> + </repeat> + + <param argument="--maxLibraryInsertSize" type="integer" optional="true" value="" label="Maximum library insert size defines different cut offs based on the maximum expected library size" help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer) + which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates + belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate + is too far away from the nearest restriction site." /> + + <repeat name="binSizes" title="Bin size in bp" min="1" help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites. + Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file."> + <param argument="--binSize" type="integer" optional="true" value="" label="Bin size in bp" /> + </repeat> + + <expand macro="region" /> + <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." /> + <expand macro="minMappingQuality" /> + <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." /> + <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected + Usually the sizes can be determined from the SAM/BAM input files, however, + for cHi-C or scHi-C it can be that at the start or end no data is present. + Please consider that this option causes that only reads are considered which are on the listed chromosomes. + Use this option to guarantee fixed sizes. An example file is available via UCSC: + http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" /> + <param name="dbKey" type="text" optional="true" label="Use this dbkey for your history genome" + help="You can set the reference genome in your history as metadata. In case you have not you can specify it here." /> + + <param argument="--outBam" type="boolean" truevalue="--outBam" falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam + file containing all valid Hi-C reads can be created + using this option. This bam file could be useful to + inspect the distribution of valid Hi-C reads pairs or + for other downstream analyses, but is not used by any + HiCExplorer tool. Computation will be significantly + longer if this option is set." /> + + <param name="outputFormat" type="select" label="Output file format"> + <option value="h5">HiCExplorer format</option> + <option value="cool">cool</option> + </param> + </inputs> + <outputs> + <data name="outfileBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"> + <filter>outBam</filter> + </data> + <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}"> + <change_format> + <when input="outputFormat" value="cool" format="cool" /> + </change_format> + </data> + <data name="qc" format="html" label="${tool.name} QC on ${on_string}" /> + <data name="raw_qc" from_work_dir="raw_qc" format="txt" label="${tool.name} raw QC on ${on_string}" /> + </outputs> + <tests> + <test expect_num_outputs="4"> + <repeat name="samFiles"> + <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" /> + </repeat> + <repeat name="samFiles"> + <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" /> + </repeat> + <param name="outputFormat" value="h5" /> + <repeat name="binSizes"> + <param name="binSize" value="5000" /> + </repeat> + <param name="outBam" value="True" /> + <output name="outfileBam" file="small_test_matrix_result_sorted_microc.bam" compare="diff" lines_diff="2" ftype="bam" /> + <output name="outFileName" ftype="h5"> + <assert_contents> + <has_h5_keys keys="intervals,matrix" /> + </assert_contents> + </output> + <output name="raw_qc" file="raw_qc_report_micro-c" compare="diff" lines_diff="2" /> + </test> + <test expect_num_outputs="4"> + <repeat name="samFiles"> + <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" /> + </repeat> + <repeat name="samFiles"> + <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" /> + </repeat> + <repeat name="binSizes"> + <param name="binSize" value="5000" /> + </repeat> + <param name="outputFormat" value="cool" /> + <param name="outBam" value="True" /> + <output name="outfileBam" file="small_test_matrix_result_sorted_microc.bam" compare="diff" lines_diff="2" ftype="bam" /> + <output name="outFileName" ftype="cool"> + <assert_contents> + <has_h5_keys keys="bins,chroms,indexes,pixels" /> + </assert_contents> + </output> + <output name="raw_qc" file="raw_qc_report_micro-c" compare="diff" lines_diff="2" /> + </test> + </tests> + <help><![CDATA[ + +Creation of the contact matrix +=============================== + + +**hicBuildMatrixMicroC** generates a contact matrix from Micro-C read pairs, using paired-end Hi-C reads mapped to a reference genome. This process requires two SAM or BAM files: one for the first mate and one for the second mate of the paired-end reads. These files must be unaligned by position (i.e., not sorted). Unlike traditional Hi-C data, where restriction enzyme cut sites determine resolution, Micro-C does not rely on such sites. Instead, the contact matrix is created using a fixed bin size (e.g., 10,000 bp). + +Additionally, **hicBuildMatrixMicroC** produces a quality control report to evaluate the quality of the Hi-C reads, aiding in determining the success of both the experimental protocol and sequencing process. + + +_________________ + + +Usage +----- + + +This tool is designed to work with paired SAM/BAM files generated by alignment software supporting local alignment, such as Bowtie2, using the `--local` alignment option for paired-end reads. Both files should represent properly mapped reads. + +_________________ + + +Output +------ + +**hicBuildMatrixMicroC** generates the following outputs: + +- **Contact Matrix**: A matrix compatible with HiCExplorer for downstream analyses. +- **Accepted Alignments BAM File**: This file includes valid Hi-C read pairs. While not directly used by HiCExplorer, it is valuable for inspecting the distribution of valid reads, such as around restriction enzyme sites, or for other analyses. +- **Quality Control Report**: This report provides an evaluation of the Hi-C data, helping to determine whether the library preparation and experimental workflow were successful. + + +Example plot +++++++++++++ + +.. image:: hicPlotMatrix.png + :width: 50% + +*Contact matrix of *Drosophila melanogaster* embryos built using **hicBuildMatrix**. The example shows Micro-C data, visualized with `hicPlotMatrix`. Bins were merged to a 25 kb resolution using `hicMergeMatrixBins` before plotting.* + + + + +Quality report +++++++++++++++ + +A detailed quality control report accompanies the contact matrix. This report is similar to the one generated by **hicBuildMatrix**, but excludes information specific to restriction cut sites, such as dangling ends and self-circles, as these features are not applicable to Micro-C data. + + +_________________ + +| For more information about HiCExplorer please consider our documentation on readthedocs.io_. + +.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html +]]> </help> + <expand macro="citations" /> +</tool>