Mercurial > repos > bgruening > deeptools_compute_matrix_operations
changeset 0:1638c02b28b5 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatrixOperations.xml Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,179 @@ +<tool id="deeptools_compute_matrix_operations" name="computeMatrixOperations" version="@WRAPPER_VERSION@.0"> + <description>Modify or combine the output of computeMatrix in a variety of ways.</description> + <macros> + <token name="@BINARY@">computeMatrixOperations</token> + <import>deepTools_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command> +<![CDATA[ + @BINARY@ + #if $submodule.command == "info": + info + -m $submodule.matrixFile + > $outFileTxt + #else if $submodule.command == "subset": + subset + -m $submodule.matrixFile + #if $submodule.groups is not None and str($submodule.groups) != '': + --groups $submodule.groups + #end if + #if $submodule.samples is not None and str($submodule.samples) != '': + --samples $submodule.samples + #end if + -o $outFileName + #else if $submodule.command == "filterStrand": + filterStrand + -m $submodule.matrixFile + --strand $submodule.strand + -o $outFileName + #else if $submodule.command == "rbind": + #set $files=[] + #for $f in $submodule.matrixFiles: + #silent $files.append(str($f.matrixFile)) + #end for + rbind + -m '#echo "' '".join($files)#' + -o $outFileName + #else if $submodule.command == "cbind": + cbind + #set $files=[] + #for $f in $submodule.matrixFiles: + #silent $files.append(str($f.matrixFile)) + #end for + -m '#echo "' '".join($files)#' + -o $outFileName + #else if $submodule.command == "sort": + sort + #set $files=[] + #for $f in $submodule.regionsFiles: + #silent $files.append(str($f.regionsFile)) + #end for + -m $submodule.matrixFile + -R '#echo "' '".join($files)#' + -o $outFileName + #end if +]]> + </command> + <inputs> + <conditional name="submodule"> + <param name="command" type="select" label="Operation type"> + <option value="info" selected="true">Print information (info)</option> + <option value="subset">Subset by samples and/or groups of regions (subset)</option> + <option value="filterStrand">Filter by strand (filterStrand)</option> + <option value="rbind">Bind matrices, top to bottom (rbind)</option> + <option value="cbind">Bind matrices, left to right (cbind)</option> + <option value="sort">Sort by region order in specified files (sort)</option> + </param> + <when value="info"> + <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" + label="Matrix file from the computeMatrix tool" help=""/> + </when> + + <when value="subset"> + <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" + label="Matrix file from the computeMatrix tool" help=""/> + <param argument="groups" type="text" optional="true" label="Region groups to include." + help="If blank, all region groups are output. Alternatively, one or more groups listed in the output of the 'info' command can be used (separate groups by a space and enclose in quotes if needed)" /> + <param argument="samples" type="text" optional="true" label="Samples to include." + help="If blank, all samples are output. Alternatively, one or more samples listed in the output of the 'info' command can be used (separate sample names by a space and enclose in quotes if needed)" /> + </when> + + <when value="filterStrand"> + <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" + label="Matrix file from the computeMatrix tool" help=""/> + <param argument="strand" type="select" label="Only include regions on this strand." + help="Only regions on the desired strand will be included in the output. If you desire to instead remove regions on only one strand (or the . strand), separately run this on the other strand and then use the rbind operation."> + <option value="+">+</option> + <option value="-">-</option> + <option value=".">. (no annotated strand)</option> + </param> + </when> + + <when value="rbind"> + <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2"> + <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" + label="Matrix file from the computeMatrix tool" help=""/> + </repeat> + </when> + + <when value="cbind"> + <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2"> + <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" + label="Matrix file from the computeMatrix tool" help=""/> + </repeat> + </when> + + <when value="sort"> + <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" + label="Matrix file from the computeMatrix tool" help=""/> + <repeat name="regionsFiles" title="BED or GTF files of regions" min="1"> + <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot" + help="File, in BED format, containing the regions to plot."/> + </repeat> + </when> + </conditional> + </inputs> + <outputs> + <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} ${submodule.command} on ${on_string}"> + <filter> + (( + submodule['command'] != "info" + )) + </filter> + </data> + <data format="txt" name="outFileTxt" label="${tool.name} info on ${on_string}"> + <filter> + (( + submodule['command'] == "info" + )) + </filter> + </data> + </outputs> + <tests> + <test> + <param name="command" value="info" /> + <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> + <output name="outFileTxt" file="computeMatrixOperations.txt" ftype="txt" /> + </test> + <test> + <param name="command" value="rbind" /> + <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> + <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" /> + <output name="outFileName" file="computeMatrixOperations_result2.mat.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" delta="100"/> + </test> + </tests> + <help> +<![CDATA[ + +What it does +------------ + +``computeMatrixOperations`` can perform a variety of operations on one or more files produced by ``computeMatrix`` (N.B., the output is always written to a new file): + ++----------------+--------------------------------------------------------------------------------------------------------------------------+ ++ **Subcommand** | **What it does** | ++----------------+--------------------------------------------------------------------------------------------------------------------------+ ++ info | Prints out the sample and region group names in the order in which they appear. | ++----------------+--------------------------------------------------------------------------------------------------------------------------+ ++ subset | Subsets a file by the desired samples/region group names. This can also change the order of these samples/region groups. | ++----------------+--------------------------------------------------------------------------------------------------------------------------+ ++ filterStrand | Filters the file to only include regions annotated as being on a particular strand. | ++----------------+--------------------------------------------------------------------------------------------------------------------------+ ++ rbind | Concatenates multiple matrices together, top to bottom. | ++----------------+--------------------------------------------------------------------------------------------------------------------------+ ++ cbind | Merges multiple matrices, left to right. | ++----------------+--------------------------------------------------------------------------------------------------------------------------+ ++ sort | Sorts the given file so regions are in the order of occurence in the input BED/GTF file(s). | ++----------------+--------------------------------------------------------------------------------------------------------------------------+ + + +These operations are useful when you want to run computeMatrix on multiple files (thereby keeping all of the values together) and later exclude regions/samples or add new ones. Another common use would be if you require the output of computeMatrix to be sorted to match the order of regions in the input file. + +----- + +@REFERENCES@ +]]> + </help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/datatypes_conf.xml Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<datatypes> + <registration> + <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/> + <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/> + </registration> +</datatypes>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,811 @@ +<macros> + + <xml name="advancedOpt_scaffold"> + <conditional name="advancedOpt"> + <param name="showAdvancedOpt" type="select" label="Show advanced options" > + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no" /> + <when value="yes"> + <yield/> + </when> + </conditional> + </xml> + + <token name="@ADVANCED_OPTS_READ_PROCESSING@"> + #if $advancedOpt.doExtendCustom.doExtend == 'custom': + --extendReads $advancedOpt.doExtendCustom.extendReadsValue + #else if $advancedOpt.doExtendCustom.doExtend == 'yes': + --extendReads + #end if + $advancedOpt.ignoreDuplicates + $advancedOpt.centerReads + #if $advancedOpt.minMappingQuality: + --minMappingQuality '$advancedOpt.minMappingQuality' + #end if + #if $advancedOpt.samFlagInclude: + --samFlagInclude $advancedOpt.samFlagInclude + #end if + #if $advancedOpt.samFlagExclude: + --samFlagExclude $advancedOpt.samFlagExclude + #end if + #if $advancedOpt.minFragmentLength: + --minFragmentLength $advancedOpt.minFragmentLength + #end if + #if $advancedOpt.maxFragmentLength: + --maxFragmentLength $advancedOpt.maxFragmentLength + #end if + </token> + + <token name="@ADVANCED_OPTS_GTF@"> + $advancedOpt.metagene + #if $advancedOpt.transcriptID: + --transcriptID $advancedOpt.transcriptID + #end if + #if $advancedOpt.exonID: + --exonID $advancedOpt.exonID + #end if + #if $advancedOpt.transcript_id_designator: + --transcript_id_designator $advancedOpt.transcript_id_designator + #end if + </token> + + <xml name="heatmap_options"> + <expand macro="zMin_zMax" /> + <expand macro="colorMap" /> + <expand macro="plotTitle" /> + <expand macro="plotNumbers" /> + </xml> + + <token name="@HEATMAP_OPTIONS@"> + #if str($plotting_type.zMin) != "": + --zMin $plotting_type.zMin + #end if + #if str($plotting_type.zMax) != "": + --zMax $plotting_type.zMax + #end if + --colorMap '$plotting_type.colorMap' + $plotting_type.plotNumbers + --plotTitle '$plotting_type.plotTitle' + </token> + + + <xml name="includeZeros"> + <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" + label="Include zeros" + help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." /> + </xml> + + <xml name="zMin_zMax"> + <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities" + help="If not specified the value is set automatically."/> + <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities" + help="If not specified the value is set automatically."/> + </xml> + + <xml name="region_limit_operation"> + <param argument="--region" type="text" value="" + label="Region of the genome to limit the operation to" + help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"."> + <sanitizer> + <valid initial="string.letters,string.digits"> + <add value="|"/> + <add value=":"/> + </valid> + </sanitizer> + </param> + </xml> + + <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> + <token name="@WRAPPER_VERSION@">2.4.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.7.10">python</requirement> + <requirement type="package" version="2.4.1">deeptools</requirement> + <yield /> + </requirements> + <expand macro="stdio" /> + <version_command>@BINARY@ --version</version_command> + </xml> + + <xml name="smoothLength"> + <param argument="--smoothLength" type="integer" value="" optional="True" min="1" + label="Smooth values using the following length (in bases)" + help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> + </xml> + + + <xml name="kmeans_clustering"> + <conditional name="used_multiple_regions"> + <param name="used_multiple_regions_options" type="select" + label="Did you compute the matrix with more than one groups of regions?" + help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> + <option value="yes">Yes, I used multiple groups of regions</option> + <option value="no">No, I used only one group</option> + </param> + <when value="no"> + <conditional name="clustering"> + <param name="clustering_options" type="select" label="Clustering algorithm"> + <option value="none">No clustering</option> + <option value="kmeans">Kmeans clustering</option> + <option value="hclust">Hierarchical clustering</option> + </param> + <when value="kmeans"> + <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" + help="When this option is set, the matrix is split into clusters using the k-means algorithm. + This only works for data that is not grouped, otherwise only the first group will be clustered. + If more specific clustering methods are required it is advisable to save the underlying matrix and + run the clustering using other software."/> + </when> + <when value="hclust"> + <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." + help="WARNING: This option causes the tool to run for a very long time! When this option is + set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. + This only works for data that is not grouped, otherwise only the first group will be clustered. + Note that you must have used the '--missingDataAsZero' option within computeMatrix! + If more specific clustering methods are required it is advisable to save the underlying matrix and + run the clustering using other software."/> + </when> + <when value="none" /> + </conditional> + </when> + <when value="yes" /> + </conditional> + </xml> + + <token name="@KMEANS_CLUSTERING@"> + #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': + #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: + --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans + #end if + #end if + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': + #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: + --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust + #end if + #end if + #end if + </token> + + <xml name="samFlags"> + <param argument="--samFlagInclude" type="integer" optional="True" value="" + label="Include reads based on the SAM flag" + help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/> + <param argument="--samFlagExclude" type="integer" optional="True" value="" + label="Exclude reads based on the SAM flag" + help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/> + </xml> + + <xml name="fragLength"> + <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0" + label="Minimum fragment length for inclusion." + help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." /> + <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0" + label="Maximum fragment length for inclusion." + help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." /> + </xml> + + <xml name="read_processing_options"> + <expand macro="extendReads" /> + <expand macro="ignoreDuplicates" /> + <expand macro="centerReads" /> + <expand macro="minMappingQuality" /> + <expand macro="samFlags" /> + <expand macro="fragLength" /> + </xml> + + <xml name="gtf_options"> + <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue="" + label="Use a metagene model" + help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." /> + <param argument="--transcriptID" optional="True" value="transcript" type="text" + label="trascript designator" + help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" /> + <param argument="--exonID" optional="True" value="exon" type="text" + label="exon designator" + help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" /> + <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text" + label="transcriptID key designator" + help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists) + or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g., + as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be + convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" /> + </xml> + + + <xml name="plotNumbers"> + <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" + label="Plot the correlation value" + help="If set, then the correlation number is plotted on top of the heatmap."/> + </xml> + + <xml name="extendReads"> + <conditional name="doExtendCustom"> + <param name="doExtend" type="select" label="Extend reads to the given average fragment size." + help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here. + By default *each* read mate is extended. + This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. + Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. + Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not + recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> + <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> + <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> + <option value="custom">A custom length, which will be applied to ALL reads.</option> + </param> + <when value="no" /> + <when value="yes" /> + <when value="custom"> + <param name="extendReadsValue" type="integer" value="300" min="1" + label="Extend reads to the given average fragment size" + help="Extend all reads to this length" /> + </when> + </conditional> + </xml> + + <xml name="corMethod"> + <param argument="--corMethod" type="select" label="Correlation method"> + <option value="spearman" selected="True">Spearman</option> + <option value="pearson">Pearson</option> + </param> + </xml> + + <xml name="distanceBetweenBins"> + <param argument="--distanceBetweenBins" type="integer" value="0" min="0" + label="Distance between bins" + help="By default, multiBamSummary considers consecutive bins of + the specified 'Bin size'. However, to reduce the + computation time, a larger distance between bins can + be given. Larger distances result in fewer bins being + considered."/> + </xml> + + <xml name="centerReads"> + <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" + label="Center regions with respect to the fragment length" + help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/> + </xml> + + <xml name="ignoreDuplicates"> + <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" + label="Ignore duplicates" + help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> + </xml> + + <xml name="sortUsing"> + <param argument="--sortUsing" type="select" label="Method used for sorting" + help="For each row the method is computed."> + <option value="mean" selected="true">mean</option> + <option value="median">median</option> + <option value="min">min</option> + <option value="max">max</option> + <option value="sum">sum</option> + <option value="region_length">region length</option> + </param> + </xml> + + <xml name="sortRegionsComputeMatrix"> + <param argument="--sortRegions" type="select" label="Sort regions" + help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> + <option value="no">no ordering</option> + <option value="keep" selected="true">maintain the same ordering as the input files</option> + <option value="descend">descending order</option> + <option value="ascend">ascending order</option> + </param> + </xml> + + <xml name="sortRegions"> + <param argument="--sortRegions" type="select" label="Sort regions" + help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> + <option value="no">no ordering</option> + <option value="descend">descending order</option> + <option value="ascend">ascending order</option> + </param> + </xml> + + <xml name="minMappingQuality"> + <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0" + label="Minimum mapping quality" + help= "If set, only reads with a mapping quality score higher than this value are considered."/> + </xml> + + <xml name="skipZeros"> + <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" + label ="Skip zeros" + help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." /> + </xml> + + <xml name="fragmentLength"> + <param argument="--fragmentLength" type="integer" value="300" min="1" + label="Fragment length used for the sequencing" + help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/> + </xml> + + <xml name="scaleFactor"> + <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" + help="When used in combination with --normalizeTo1x or + --normalizeUsingRPKM, the computed scaling factor will + be multiplied by the given scale factor." /> + </xml> + + <xml name="scaleFactors"> + <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> + <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + <regex match="EXception:" /> + <regex match="Traceback" /> + </stdio> + </xml> + + <xml name="pseudocount"> + <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> + </xml> + + <token name="@REFERENCES@"> + +.. class:: infomark + +For more information on the tools, please visit our `help site`_. + +If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com + +This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. + +.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac +.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de +.. _help site: https://deeptools.readthedocs.org/ + + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/nar/gkw257</citation> + <yield /> + </citations> + </xml> + + <xml name="multiple_input_bams"> + <conditional name="multibam_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bamfiles" type="data" format="bam" min="1" + label="Bam file" multiple="true" + help=""/> + </when> + <when value="Yes"> + <repeat name="multibam_repeats" min="1" title="BAM Files"> + <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> + </repeat> + </when> + </conditional> + </xml> + + <xml name="multiple_input_bams_min2"> + <conditional name="multibam_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples +is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bamfiles" type="data" format="bam" min="2" + label="Bam file" multiple="true" + help=""/> + </when> + <when value="Yes"> + <repeat name="multibam_repeats" min="2" title="BAM Files"> + <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> + </repeat> + </when> + </conditional> + </xml> + + <xml name="multiple_input_bigwigs"> + <conditional name="multibigwig_conditional"> + <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples +is vital to you, select Yes below."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"> + <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" + label="Bigwig file" + help="A Bigwig file."/> + </when> + <when value="Yes"> + <repeat name="multibigwig_repeats" min="2" title="BigWig files"> + <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/> + </repeat> + </when> + </conditional> + </xml> + + <xml name="plotTitle"> + <param argument="--plotTitle" type="text" value="" size="30" optional="True" + label="Title of the plot" + help="Title of the plot, to be printed on top of the generated image." /> + </xml> + + + <token name="@multiple_input_bams@"> +<![CDATA[ + #set files=[] + #set labels=[] + #if $multibam_conditional.orderMatters == "No": + #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): + ln -s "${bamfile}" "./${counter}.bam" && + ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && + #silent $files.append('%s.bam' % $counter) + #silent $labels.append("'%s'" % ($bamfile.display_name)) + #end for + #else: + #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): + ln -s "${f.bamfile}" "./${counter}.bam" && + ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" && + #silent $files.append('%s.bam' % $counter) + #silent $labels.append("'%s'" % ($f.bamfile.display_name)) + #end for + #end if +]]> + </token> + + <token name="@multiple_input_bigwigs@"> +<![CDATA[ + #set files=[] + #set labels=[] + #if $multibigwig_conditional.orderMatters == "No": + #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): + ln -s "${bigwig}" "${counter}.bw" && + #silent $files.append('%s.bw' % $counter) + #silent $labels.append("'%s'" % ($bigwig.display_name)) + #end for + #else: + #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): + ln -s "${f.bigwig}" "${counter}.bw" && + #silent $files.append('%s.bw' % $counter) + #silent $labels.append("'%s'" % ($f.bigwig.display_name)) + #end for + #end if +]]> + </token> + + <xml name="blacklist"> + <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0" + label="Blacklisted regions in BED/GTF format" + help="One or more files containing regions to exclude from the analysis" /> + </xml> + + <token name="@blacklist@"> +<![CDATA[ + #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None': + #set blfiles=[] + #for $f in $advancedOpt.blackListFileName: + #silent $blfiles.append("'%s'" % $f) + #end for + #if $blfiles != ["'None'"]: + --blackListFileName #echo ' '.join($blfiles)# + #end if + #end if +]]> + </token> + + <xml name="multiple_bed"> + <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true" + label="Regions in BED/GTF format" + help="One or more files containing regions to include in the analysis" /> + </xml> + + <token name="@multiple_bed@"> +<![CDATA[ + #set files=[] + #set labels=[] + #for $f in $BED: + #silent $files.append("'%s'" % $f) + #silent $labels.append("'%s'" % $f.display_name) + #end for + #if len($files) > 0: + --BED #echo ' '.join($files)# + --regionLabels #echo ' '.join($labels)# + #end if +]]> + </token> + + <xml name="reference_genome_source"> + <conditional name="source"> + <param name="ref_source" type="select" label="Reference genome"> + <option value="cached">locally cached</option> + <option value="history">in your history</option> + </param> + <when value="cached"> + <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_data_table="lastz_seqs"> + <filter type="sort_by" column="1" /> + <validator type="no_options" message="No indexes are available." /> + </options> + </param> + </when> + <when value="history"> + <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> + </when> + </conditional> + </xml> + + <token name="@reference_genome_source@"> + #if $source.ref_source=="history": + --genome $source.input1 + #else: + --genome "$source.input1_2bit.fields.path" + #end if + </token> + + <xml name="effectiveGenomeSize"> + <conditional name="effectiveGenomeSize"> + <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" + help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. + Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. + See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> + <option value="93260000">ce10 (93260000)</option> + <option value="121400000">dm3 (121400000)</option> + <option value="2451960000" selected="true">hg19 (2451960000)</option> + <option value="2150570000">mm9 (2150570000)</option> + <option value="specific">user specified</option> + </param> + <when value="specific"> + <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" + help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> + </when> + <when value="2150570000" /> + <when value="2451960000" /> + <when value="121400000" /> + <when value="93260000" /> + </conditional> + </xml> + + <xml name="skipNAs"> + <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" + label="Ignore missing data?" + help="This parameter determines if non-covered regions + (regions without overlapping reads) in a bam/bigWig file + should be skipped. The default is to treat those + regions as having a value of zero. The decision to + skip non-covered regions depends on the interpretation + of the data. Non-covered regions may represent, for + example, repetitive regions that should be ignored. + (default: False)" /> + </xml> + + <xml name="input_save_matrix_values"> + <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> + </xml> + + <xml name="input_graphic_output_settings"> + <conditional name="output" > + <param name="showOutputSettings" type="select" label="Show advanced output settings" > + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no" /> + <when value="yes"> + <yield /> + <param name="saveSortedRegions" type="boolean" + label="Save the regions after skipping zeros or min/max threshold values" + help="The order of the regions in the file follows the sorting order selected. This is useful, + for example, to generate other heatmaps keeping the sorting of the first heatmap."/> + </when> + </conditional> + </xml> + + + <xml name="input_image_file_format"> + <param argument="--outFileFormat" type="select" label="Image file format"> + <option value="png" selected="true">png</option> + <option value="pdf">pdf</option> + <option value="svg">svg</option> + <option value="eps">eps</option> + </param> + </xml> + + <xml name="output_dpi"> + <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True" + label="Image dpi" help=""/> + </xml> + + <xml name="output_image_file_format"> + <data format="png" name="outFileName" label="${tool.name} image"> + <change_format> + <when input="output.outFileFormat" value="pdf" format="pdf" /> + <when input="output.outFileFormat" value="svg" format="svg" /> + <when input="output.outFileFormat" value="eps" format="eps" /> + </change_format> + </data> + </xml> + + <xml name="output_image_file_format_not_nested"> + <data format="png" name="outFileName" label="${tool.name} image"> + <change_format> + <when input="outFileFormat" value="pdf" format="pdf" /> + <when input="outFileFormat" value="svg" format="svg" /> + <when input="outFileFormat" value="eps" format="eps" /> + </change_format> + </data> + </xml> + + <xml name="output_save_matrix_values"> + <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveMatrix'] is True + )) + </filter> + </data> + </xml> + + <xml name="output_graphic_outputs"> + <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveSortedRegions'] is True + )) + </filter> + </data> + </xml> + + <xml name="colorMap"> + <param name="colorMap" type="select" label="Color map to use for the heatmap" + help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html" + multiple="true"> + <option value="RdYlBu" selected="true">RdYlBu</option> + <option value="Accent">Accent</option> + <option value="Spectral">Spectral</option> + <option value="Set1">Set1</option> + <option value="Set2">Set2</option> + <option value="Set3">Set3</option> + <option value="Dark2">Dark2</option> + <option value="Reds">Reds</option> + <option value="Oranges">Oranges</option> + <option value="Greens">Greens</option> + <option value="Blues">Blues</option> + <option value="Greys">Greys</option> + <option value="Purples">Purples</option> + <option value="Paired">Paired</option> + <option value="Pastel1">Pastel1</option> + <option value="Pastel2">Pastel2</option> + <option value="spring">spring</option> + <option value="summer">summer</option> + <option value="autumn">autumn</option> + <option value="winter">winter</option> + <option value="hot">hot</option> + <option value="coolwarm">coolwarm</option> + <option value="cool">cool</option> + <option value="seismic">seismic</option> + <option value="terrain">terrain</option> + <option value="ocean">ocean</option> + <option value="rainbow">rainbow</option> + <option value="bone">bone</option> + <option value="flag">flag</option> + <option value="prism">prism</option> + <option value="cubehelix">cubehelix</option> + <option value="binary">binary</option> + <option value="pink">pink</option> + <option value="gray">gray</option> + <option value="copper">copper</option> + <option value="BrBG">BrBG</option> + <option value="BuGn">BuGn</option> + <option value="BuPu">BuPu</option> + <option value="GnBu">GnBu</option> + <option value="OrRd">OrRd</option> + <option value="PiYG">PiYG</option> + <option value="PRGn">PRGn</option> + <option value="PuOr">PuOr</option> + <option value="PuRd">PuRd</option> + <option value="PuBu">PuBu</option> + <option value="RdBu">RdBu</option> + <option value="RdGy">RdGy</option> + <option value="RdPu">RdPu</option> + <option value="YlGn">YlGn</option> + <option value="PuBuGn">PuBuGn</option> + <option value="RdYlGn">RdYlGn</option> + <option value="YlGnBu">YlGnBu</option> + <option value="YlOrBr">YlOrBr</option> + <option value="YlOrRd">YlOrRd</option> + <option value="gist_gray">gist_gray</option> + <option value="gist_stern">gist_stern</option> + <option value="gist_earth">gist_earth</option> + <option value="gist_yarg">gist_yarg</option> + <option value="gist_ncar">gist_ncar</option> + <option value="gist_rainbow">gist_rainbow</option> + <option value="gist_heat">gist_heat</option> + <option value="gnuplot">gnuplot</option> + <option value="gnuplot2">gnuplot2</option> + <option value="CMRmap">CMRmap</option> + <option value="bwr">bwr</option> + <option value="hsv">hsv</option> + <option value="brg">brg</option> + <option value="jet">jet</option> + <option value="afmhot">afmhot</option> + <option value="Accent_r">Accent reversed</option> + <option value="Spectral_r">Spectral reversed</option> + <option value="Set1_r">Set1 reversed</option> + <option value="Set2_r">Set2 reversed</option> + <option value="Set3_r">Set3 reversed</option> + <option value="Dark2_r">Dark2 reversed</option> + <option value="Reds_r">Reds reversed</option> + <option value="Oranges_r">Oranges reversed</option> + <option value="Greens_r">Greens reversed</option> + <option value="Blues_r">Blues reversed</option> + <option value="Greys_r">Greys reversed</option> + <option value="Purples_r">Purples reversed</option> + <option value="Paired_r">Paired reversed</option> + <option value="Pastel1_r">Pastel1 reversed</option> + <option value="Pastel2_r">Pastel2 reversed</option> + <option value="spring_r">spring reversed</option> + <option value="summer_r">summer reversed</option> + <option value="autumn_r">autumn reversed</option> + <option value="winter_r">winter reversed</option> + <option value="hot_r">hot reversed</option> + <option value="coolwarm_r">coolwarm reversed</option> + <option value="cool_r">cool reversed</option> + <option value="seismic_r">seismic reversed</option> + <option value="terrain_r">terrain reversed</option> + <option value="ocean_r">ocean reversed</option> + <option value="rainbow_r">rainbow reversed</option> + <option value="bone_r">bone reversed</option> + <option value="flag_r">flag reversed</option> + <option value="prism_r">prism reversed</option> + <option value="cubehelix_r">cubehelix reversed</option> + <option value="binary_r">binary reversed</option> + <option value="pink_r">pink reversed</option> + <option value="gray_r">gray reversed</option> + <option value="copper_r">copper reversed</option> + <option value="BrBG_r">BrBG reversed</option> + <option value="BuGn_r">BuGn reversed</option> + <option value="BuPu_r">BuPu reversed</option> + <option value="GnBu_r">GnBu reversed</option> + <option value="OrRd_r">OrRd reversed</option> + <option value="PiYG_r">PiYG reversed</option> + <option value="PRGn_r">PRGn reversed</option> + <option value="PuOr_r">PuOr reversed</option> + <option value="PuRd_r">PuRd reversed</option> + <option value="PuBu_r">PuBu reversed</option> + <option value="RdBu_r">RdBu reversed</option> + <option value="RdGy_r">RdGy reversed</option> + <option value="RdPu_r">RdPu reversed</option> + <option value="YlGn_r">YlGn reversed</option> + <option value="PuBuGn_r">PuBuGn reversed</option> + <option value="RdYlBu_r">RdYlBu reversed</option> + <option value="RdYlGn_r">RdYlGn reversed</option> + <option value="YlGnBu_r">YlGnBu reversed</option> + <option value="YlOrBr_r">YlOrBr reversed</option> + <option value="YlOrRd_r">YlOrRd reversed</option> + <option value="gist_gray_r">gist_gray reversed</option> + <option value="gist_stern_r">gist_stern reversed</option> + <option value="gist_earth_r">gist_earth reversed</option> + <option value="gist_yarg_r">gist_yarg reversed</option> + <option value="gist_ncar_r">gist_ncar reversed</option> + <option value="gist_rainbow_r">gist_rainbow reversed</option> + <option value="gist_heat_r">gist_heat reversed</option> + <option value="gnuplot_r">gnuplot reversed</option> + <option value="gnuplot2_r">gnuplot2 reversed</option> + <option value="CMRmap_r">CMRmap reversed</option> + <option value="bwr_r">bwr reversed</option> + <option value="hsv_r">hsv reversed</option> + <option value="brg_r">brg reversed</option> + <option value="jet_r">jet reversed</option> + <option value="afmhot_r">afmhot reversed</option> + </param> + + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deepTools_macros.xml.orig Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,639 @@ +<macros> + + <xml name="advancedOpt_scaffold"> + <conditional name="advancedOpt"> + <param name="showAdvancedOpt" type="select" label="Show advanced options" > + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no" /> + <when value="yes"> + <yield/> + </when> + </conditional> + </xml> + + <token name="@ADVANCED_OPTS_READ_PROCESSING@"> + #if $advancedOpt.doExtendCustom.doExtend == 'custom': + --extendReads $advancedOpt.doExtendCustom.extendReadsValue + #else if $advancedOpt.doExtendCustom.doExtend == 'yes': + --extendReads + #end if + $advancedOpt.ignoreDuplicates + $advancedOpt.centerReads + #if $advancedOpt.minMappingQuality: + --minMappingQuality '$advancedOpt.minMappingQuality' + #end if + #if $advancedOpt.samFlagInclude: + --samFlagInclude $advancedOpt.samFlagInclude + #end if + #if $advancedOpt.samFlagExclude: + --samFlagExclude $advancedOpt.samFlagExclude + #end if + </token> + + <xml name="heatmap_options"> + <expand macro="zMin_zMax" /> + <expand macro="colorMap" /> + <expand macro="plotTitle" /> + <expand macro="plotNumbers" /> + </xml> + + <token name="@HEATMAP_OPTIONS@"> + #if str($plotting_type.zMin) != "": + --zMin $plotting_type.zMin + #end if + #if str($plotting_type.zMax) != "": + --zMax $plotting_type.zMax + #end if + --colorMap '$plotting_type.colorMap' + $plotting_type.plotNumbers + --plotTitle '$plotting_type.plotTitle' + </token> + + + <xml name="includeZeros"> + <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" + label="Include zeros" + help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." /> + </xml> + + <xml name="zMin_zMax"> + <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities" + help="If not specified the value is set automatically."/> + <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities" + help="If not specified the value is set automatically."/> + </xml> + + <xml name="region_limit_operation"> + <param argument="--region" type="text" value="" + label="Region of the genome to limit the operation to" + help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." /> + </xml> + + <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> +<<<<<<< HEAD + <token name="@WRAPPER_VERSION@">2.0.1.0</token> +======= + <token name="@WRAPPER_VERSION@">2.1.0</token> +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.7.10">python</requirement> + <requirement type="binary">@BINARY@</requirement> +<<<<<<< HEAD + <requirement type="package" version="2.0.1">deepTools</requirement> +======= + <requirement type="package" version="2.1.0">deepTools</requirement> +>>>>>>> d56067f86089e75354a2fad266002db3730766d9 + <yield /> + </requirements> + <expand macro="stdio" /> + <version_command>@BINARY@ --version</version_command> + </xml> + + <xml name="smoothLength"> + <param argument="--smoothLength" type="integer" value="" optional="True" min="1" + label="Smooth values using the following length (in bases)" + help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> + </xml> + + + <xml name="kmeans_clustering"> + <conditional name="used_multiple_regions"> + <param name="used_multiple_regions_options" type="select" + label="Did you compute the matrix with more than one groups of regions?" + help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions."> + <option value="yes">Yes, I used multiple groups of regions</option> + <option value="no">No, I used only one group</option> + </param> + <when value="no"> + <conditional name="clustering"> + <param name="clustering_options" type="select" label="Clustering algorithm"> + <option value="none">No clustering</option> + <option value="kmeans">Kmeans clustering</option> + <option value="hclust">Hierarchical clustering</option> + </param> + <when value="kmeans"> + <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" + help="When this option is set, the matrix is split into clusters using the k-means algorithm. + This only works for data that is not grouped, otherwise only the first group will be clustered. + If more specific clustering methods are required it is advisable to save the underlying matrix and + run the clustering using other software."/> + </when> + <when value="hclust"> + <param name="n_hclust" type="integer" value="0" label="number of clusters to compute." + help="WARNING: This option causes the tool to run for a very long time! When this option is + set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage. + This only works for data that is not grouped, otherwise only the first group will be clustered. + Note that you must have used the '--missingDataAsZero' option within computeMatrix! + If more specific clustering methods are required it is advisable to save the underlying matrix and + run the clustering using other software."/> + </when> + <when value="none" /> + </conditional> + </when> + <when value="yes" /> + </conditional> + </xml> + + <token name="@KMEANS_CLUSTERING@"> + #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': + #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: + --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans + #end if + #end if + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust': + #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0: + --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust + #end if + #end if + #end if + </token> + + <xml name="samFlags"> + <param argument="--samFlagInclude" type="integer" optional="True" value="" + label="Include reads based on the SAM flag" + help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/> + <param argument="--samFlagExclude" type="integer" optional="True" value="" + label="Exclude reads based on the SAM flag" + help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/> + </xml> + + <xml name="read_processing_options"> + <expand macro="extendReads" /> + <expand macro="ignoreDuplicates" /> + <expand macro="centerReads" /> + <expand macro="minMappingQuality" /> + <expand macro="samFlags" /> + </xml> + + <xml name="plotNumbers"> + <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" + label="Plot the correlation value" + help="If set, then the correlation number is plotted on top of the heatmap."/> + </xml> + + <xml name="extendReads"> + <conditional name="doExtendCustom"> + <param name="doExtend" type="select" label="Extend reads to the given average fragment size." + help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here. + By default *each* read mate is extended. + This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. + Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value. + Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not + recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."> + <option value="no" selected="True">No extension. The default value and most typically appropriate.</option> + <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option> + <option value="custom">A custom length, which will be applied to ALL reads.</option> + </param> + <when value="no" /> + <when value="yes" /> + <when value="custom"> + <param name="extendReadsValue" type="integer" value="300" min="1" + label="Extend reads to the given average fragment size" + help="Extend all reads to this length" /> + </when> + </conditional> + </xml> + + <xml name="corMethod"> + <param argument="--corMethod" type="select" label="Correlation method"> + <option value="spearman" selected="True">Spearman</option> + <option value="pearson">Pearson</option> + </param> + </xml> + + <xml name="distanceBetweenBins"> + <param argument="--distanceBetweenBins" type="integer" value="0" min="0" + label="Distance between bins" + help="By default, multiBamSummary considers consecutive bins of + the specified 'Bin size'. However, to reduce the + computation time, a larger distance between bins can + be given. Larger distances result in fewer bins being + considered."/> + </xml> + + <xml name="centerReads"> + <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue="" + label="Center regions with respect to the fragment length" + help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/> + </xml> + + <xml name="ignoreDuplicates"> + <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue="" + label="Ignore duplicates" + help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> + </xml> + + <xml name="sortUsing"> + <param argument="--sortUsing" type="select" label="Method used for sorting" + help="For each row the method is computed."> + <option value="mean" selected="true">mean</option> + <option value="median">median</option> + <option value="min">min</option> + <option value="max">max</option> + <option value="sum">sum</option> + <option value="region_length">region length</option> + </param> + </xml> + + <xml name="sortRegions"> + <param argument="--sortRegions" type="select" label="Sort regions" + help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> + <option value="no">no ordering</option> + <option value="descend" selected="true">descending order</option> + <option value="ascend">ascending order</option> + </param> + </xml> + + <xml name="minMappingQuality"> + <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1" + label="Minimum mapping quality" + help= "If set, only reads with a mapping quality score higher than this value are considered."/> + </xml> + + <xml name="skipZeros"> + <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" + label ="Skip zeros" + help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." /> + </xml> + + <xml name="fragmentLength"> + <param argument="--fragmentLength" type="integer" value="300" min="1" + label="Fragment length used for the sequencing" + help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/> + </xml> + + <xml name="scaleFactor"> + <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" + help="When used in combination with --normalizeTo1x or + --normalizeUsingRPKM, the computed scaling factor will + be multiplied by the given scale factor." /> + </xml> + + <xml name="scaleFactors"> + <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> + <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + <regex match="EXception:" /> + <regex match="Traceback" /> + </stdio> + </xml> + + <xml name="pseudocount"> + <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> + </xml> + + <token name="@REFERENCES@"> + +.. class:: infomark + +For more information on the tools, please visit our `help site`_. + +If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com + +This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. + +.. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac +.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de +.. _help site: https://deeptools.readthedocs.org/ + + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/nar/gku365</citation> + <yield /> + </citations> + </xml> + + <xml name="multiple_input_bams"> + <param argument="--bamfiles" type="data" format="bam" min="2" + label="Bam file" multiple="true" + help="The BAM file must be sorted."/> + </xml> + + <xml name="multiple_input_bigwigs"> + <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" + label="Bigwig file" + help="A Bigwig file."/> + </xml> + + <xml name="plotTitle"> + <param argument="--plotTitle" type="text" value="" size="30" optional="True" + label="Title of the plot" + help="Title of the plot, to be printed on top of the generated image." /> + </xml> + + + <token name="@multiple_input_bams@"> +<![CDATA[ + #set files=[] + #set labels=[] + #for $counter, $bamfile in enumerate($bamfiles): + ln -s "${bamfile}" "./${counter}.bam" && + ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && + #silent $files.append('%s.bam' % $counter) + #silent $labels.append('%s' % ($bamfile.display_name)) + #end for +]]> + </token> + + <token name="@multiple_input_bigwigs@"> +<![CDATA[ + #set files=[] + #set labels=[] + #for $counter, $bigwig in enumerate($bigwigfiles): + ln -s "${bigwig}" "${counter}.bw" && + #silent $files.append('%s.bw' % $counter) + #silent $labels.append('%s' % ($bigwig.display_name)) + #end for +]]> + </token> + + <xml name="reference_genome_source"> + <conditional name="source"> + <param name="ref_source" type="select" label="Reference genome"> + <option value="cached">locally cached</option> + <option value="history">in your history</option> + </param> + <when value="cached"> + <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_data_table="lastz_seqs"> + <filter type="sort_by" column="1" /> + <validator type="no_options" message="No indexes are available." /> + </options> + </param> + </when> + <when value="history"> + <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" /> + </when> + </conditional> + </xml> + + <token name="@reference_genome_source@"> + #if $source.ref_source=="history": + --genome $source.input1 + #else: + --genome "$source.input1_2bit.fields.path" + #end if + </token> + + <xml name="effectiveGenomeSize"> + <conditional name="effectiveGenomeSize"> + <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size" + help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. + Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. + See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes."> + <option value="93260000">ce10 (93260000)</option> + <option value="121400000">dm3 (121400000)</option> + <option value="2451960000" selected="true">hg19 (2451960000)</option> + <option value="2150570000">mm9 (2150570000)</option> + <option value="specific">user specified</option> + </param> + <when value="specific"> + <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> + </when> + <when value="2150570000" /> + <when value="2451960000" /> + <when value="121400000" /> + <when value="93260000" /> + </conditional> + </xml> + + <xml name="skipNAs"> + <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" + label="Ignore missing data?" + help="This parameter determines if non-covered regions + (regions without overlapping reads) in a bam/bigWig file + should be skipped. The default is to treat those + regions as having a value of zero. The decision to + skip non-covered regions depends on the interpretation + of the data. Non-covered regions may represent, for + example, repetitive regions that should be ignored. + (default: False)" /> + </xml> + + <xml name="input_save_matrix_values"> + <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/> + </xml> + + <xml name="input_graphic_output_settings"> + <conditional name="output" > + <param name="showOutputSettings" type="select" label="Show advanced output settings" > + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no" /> + <when value="yes"> + <yield /> + <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> + </when> + </conditional> + </xml> + + + <xml name="input_image_file_format"> + <param argument="--outFileFormat" type="select" label="Image file format"> + <option value="png" selected="true">png</option> + <option value="pdf">pdf</option> + <option value="svg">svg</option> + <option value="eps">eps</option> + </param> + </xml> + + <xml name="output_image_file_format"> + <data format="png" name="outFileName" label="${tool.name} image"> + <change_format> + <when input="output.outFileFormat" value="pdf" format="pdf" /> + <when input="output.outFileFormat" value="svg" format="svg" /> + <when input="output.outFileFormat" value="eps" format="eps" /> + </change_format> + </data> + </xml> + + <xml name="output_image_file_format_not_nested"> + <data format="png" name="outFileName" label="${tool.name} image"> + <change_format> + <when input="outFileFormat" value="pdf" format="pdf" /> + <when input="outFileFormat" value="svg" format="svg" /> + <when input="outFileFormat" value="eps" format="eps" /> + </change_format> + </data> + </xml> + + <xml name="output_save_matrix_values"> + <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveMatrix'] is True + )) + </filter> + </data> + </xml> + + <xml name="output_graphic_outputs"> + <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveSortedRegions'] is True + )) + </filter> + </data> + </xml> + + <xml name="colorMap"> + <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/"> + <option value="RdYlBu" selected="true">RdYlBu</option> + <option value="Accent">Accent</option> + <option value="Spectral">Spectral</option> + <option value="Set1">Set1</option> + <option value="Set2">Set2</option> + <option value="Set3">Set3</option> + <option value="Dark2">Dark2</option> + <option value="Reds">Reds</option> + <option value="Oranges">Oranges</option> + <option value="Greens">Greens</option> + <option value="Blues">Blues</option> + <option value="Greys">Greys</option> + <option value="Purples">Purples</option> + <option value="Paired">Paired</option> + <option value="Pastel1">Pastel1</option> + <option value="Pastel2">Pastel2</option> + <option value="spring">spring</option> + <option value="summer">summer</option> + <option value="autumn">autumn</option> + <option value="winter">winter</option> + <option value="hot">hot</option> + <option value="coolwarm">coolwarm</option> + <option value="cool">cool</option> + <option value="seismic">seismic</option> + <option value="terrain">terrain</option> + <option value="ocean">ocean</option> + <option value="rainbow">rainbow</option> + <option value="bone">bone</option> + <option value="flag">flag</option> + <option value="prism">prism</option> + <option value="cubehelix">cubehelix</option> + <option value="binary">binary</option> + <option value="pink">pink</option> + <option value="gray">gray</option> + <option value="copper">copper</option> + <option value="BrBG">BrBG</option> + <option value="BuGn">BuGn</option> + <option value="BuPu">BuPu</option> + <option value="GnBu">GnBu</option> + <option value="OrRd">OrRd</option> + <option value="PiYG">PiYG</option> + <option value="PRGn">PRGn</option> + <option value="PuOr">PuOr</option> + <option value="PuRd">PuRd</option> + <option value="PuBu">PuBu</option> + <option value="RdBu">RdBu</option> + <option value="RdGy">RdGy</option> + <option value="RdPu">RdPu</option> + <option value="YlGn">YlGn</option> + <option value="PuBuGn">PuBuGn</option> + <option value="RdYlGn">RdYlGn</option> + <option value="YlGnBu">YlGnBu</option> + <option value="YlOrBr">YlOrBr</option> + <option value="YlOrRd">YlOrRd</option> + <option value="gist_gray">gist_gray</option> + <option value="gist_stern">gist_stern</option> + <option value="gist_earth">gist_earth</option> + <option value="gist_yarg">gist_yarg</option> + <option value="gist_ncar">gist_ncar</option> + <option value="gist_rainbow">gist_rainbow</option> + <option value="gist_heat">gist_heat</option> + <option value="gnuplot">gnuplot</option> + <option value="gnuplot2">gnuplot2</option> + <option value="CMRmap">CMRmap</option> + <option value="bwr">bwr</option> + <option value="hsv">hsv</option> + <option value="brg">brg</option> + <option value="jet">jet</option> + <option value="afmhot">afmhot</option> + <option value="Accent_r">Accent reversed</option> + <option value="Spectral_r">Spectral reversed</option> + <option value="Set1_r">Set1 reversed</option> + <option value="Set2_r">Set2 reversed</option> + <option value="Set3_r">Set3 reversed</option> + <option value="Dark2_r">Dark2 reversed</option> + <option value="Reds_r">Reds reversed</option> + <option value="Oranges_r">Oranges reversed</option> + <option value="Greens_r">Greens reversed</option> + <option value="Blues_r">Blues reversed</option> + <option value="Greys_r">Greys reversed</option> + <option value="Purples_r">Purples reversed</option> + <option value="Paired_r">Paired reversed</option> + <option value="Pastel1_r">Pastel1 reversed</option> + <option value="Pastel2_r">Pastel2 reversed</option> + <option value="spring_r">spring reversed</option> + <option value="summer_r">summer reversed</option> + <option value="autumn_r">autumn reversed</option> + <option value="winter_r">winter reversed</option> + <option value="hot_r">hot reversed</option> + <option value="coolwarm_r">coolwarm reversed</option> + <option value="cool_r">cool reversed</option> + <option value="seismic_r">seismic reversed</option> + <option value="terrain_r">terrain reversed</option> + <option value="ocean_r">ocean reversed</option> + <option value="rainbow_r">rainbow reversed</option> + <option value="bone_r">bone reversed</option> + <option value="flag_r">flag reversed</option> + <option value="prism_r">prism reversed</option> + <option value="cubehelix_r">cubehelix reversed</option> + <option value="binary_r">binary reversed</option> + <option value="pink_r">pink reversed</option> + <option value="gray_r">gray reversed</option> + <option value="copper_r">copper reversed</option> + <option value="BrBG_r">BrBG reversed</option> + <option value="BuGn_r">BuGn reversed</option> + <option value="BuPu_r">BuPu reversed</option> + <option value="GnBu_r">GnBu reversed</option> + <option value="OrRd_r">OrRd reversed</option> + <option value="PiYG_r">PiYG reversed</option> + <option value="PRGn_r">PRGn reversed</option> + <option value="PuOr_r">PuOr reversed</option> + <option value="PuRd_r">PuRd reversed</option> + <option value="PuBu_r">PuBu reversed</option> + <option value="RdBu_r">RdBu reversed</option> + <option value="RdGy_r">RdGy reversed</option> + <option value="RdPu_r">RdPu reversed</option> + <option value="YlGn_r">YlGn reversed</option> + <option value="PuBuGn_r">PuBuGn reversed</option> + <option value="RdYlBu_r">RdYlBu reversed</option> + <option value="RdYlGn_r">RdYlGn reversed</option> + <option value="YlGnBu_r">YlGnBu reversed</option> + <option value="YlOrBr_r">YlOrBr reversed</option> + <option value="YlOrRd_r">YlOrRd reversed</option> + <option value="gist_gray_r">gist_gray reversed</option> + <option value="gist_stern_r">gist_stern reversed</option> + <option value="gist_earth_r">gist_earth reversed</option> + <option value="gist_yarg_r">gist_yarg reversed</option> + <option value="gist_ncar_r">gist_ncar reversed</option> + <option value="gist_rainbow_r">gist_rainbow reversed</option> + <option value="gist_heat_r">gist_heat reversed</option> + <option value="gnuplot_r">gnuplot reversed</option> + <option value="gnuplot2_r">gnuplot2 reversed</option> + <option value="CMRmap_r">CMRmap reversed</option> + <option value="bwr_r">bwr reversed</option> + <option value="hsv_r">hsv reversed</option> + <option value="brg_r">brg reversed</option> + <option value="jet_r">jet reversed</option> + <option value="afmhot_r">afmhot reversed</option> + </param> + + </xml> + +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,74 @@ +======================== +Galaxy deeptools wrapper +======================== + +deepTools are user-friendly tools for the normalization and visualization of +deep-sequencing data. +They address the challenge of visualizing the large amounts of data that are now +routinely generated from sequencing centers in a meaningful way. +To do so, deepTools contain useful routines to process the mapped reads data +through removal of duplicates and different filtering options to create coverage +files in standard bedGraph and bigWig file formats. deepTools allow the creation +of normalized coverage files or the comparison between two files +(for example, treatment and control). Finally, using such normalized and +standardized files, multiple visualizations can be created to identify +enrichments with functional annotations of the genome. +For a gallery of images that can be produced and a description +of the tools see our poster_. + +.. _poster: http://f1000.com/posters/browse/summary/1094053 + +deeptools is developed under here: + + https://github.com/fidelram/deepTools + +For support, questions, or feature requests contact: deeptools@googlegroups.com + + +============ +Installation +============ + +Requirements: python-2.7 + +Galaxy should be able to automatically install all other dependencies, such as numpy or scipy. + +For the best performance we recommend to install blas/lapack/atlas in your environment before +installing deepTools from the Tool Shed. + + +======== +Citation +======== + +deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. + + +======= +History +======= + + * v1.0: Initial public release + * v1.5.8.2: Include new citation tag, update version to 1.5.8.2 and change wrapper version + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories> + <repository changeset_revision="74b09c8e5f6e" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamCompare_result1.bg Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,1 @@ +chrM 0 16569 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamCoverage_result3.bg Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,7 @@ +chrM 0 210 9.76876e+06 +chrM 210 220 9.56092e+06 +chrM 220 230 7.6903e+06 +chrM 230 240 5.19615e+06 +chrM 240 250 3.32554e+06 +chrM 250 260 623538 +chrM 260 16569 0
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamPEFragmentSize_result1.txt Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,22 @@ + + +BAM file : 0.bam +Sample size: 3 + +Fragment lengths: +Min.: 241.0 +1st Qu.: 241.5 +Mean: 244.666666667 +Median: 242.0 +3rd Qu.: 246.5 +Max.: 251.0 +Std: 4.49691252108 + +Read lengths: +Min.: 251.0 +1st Qu.: 251.0 +Mean: 251.0 +Median: 251.0 +3rd Qu.: 251.0 +Max.: 251.0 +Std: 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bigwigCompare_result2.bg Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,3 @@ +ch1 0 400 1 +ch2 0 400 1 +ch3 0 400 1
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrix1.bed Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,8 @@ +phiX174 1000 1500 CG11023 0 + +phiX174 150 1750 cda5 0 - +phiX174 150 177 cda8 0 - +phiX174 75 1500 cda9 0 + +phiX174 101 175 C11023 0 + +phiX174 125 150 ca5 0 - +phiX174 450 1750 ca8 0 + +phiX174 80 1500 cda9 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrix2.bed Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,6 @@ +ch1 100 150 CG11023 0 + +ch2 150 175 cda5 0 - +ch3 100 125 cda8 0 + +ch1 75 125 C11023 0 + +ch2 125 150 ca5 0 - +ch3 75 100 ca8 0 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrixOperations.txt Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,4 @@ +Groups: + genes +Samples: + file_0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmapper_result2.tabular Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,3 @@ +bin labels -0.0Kb 0.0Kb +bins 1 2 +file_0 genes 2477942.34473 2610259.65234
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiBamSummary_regions.bed Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,3 @@ +chrM 1 10 +chrM 5 15 +chrM 10 20
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotCorrelation_result1.tabular Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,3 @@ + 'bowtie2-test1.bam' 'bowtie2-test1.bam' +'bowtie2-test1.bam' 1.0000 1.0000 +'bowtie2-test1.bam' 1.0000 1.0000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotCoverage_result1.tabular Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,16570 @@ +#'chr' 'start' 'end' 'bowtie2 test1.bam' 'bowtie2 test1.bam' +chrM 0 1 23.0 23.0 +chrM 1 2 35.0 35.0 +chrM 2 3 35.0 35.0 +chrM 3 4 35.0 35.0 +chrM 4 5 35.0 35.0 +chrM 5 6 35.0 35.0 +chrM 6 7 35.0 35.0 +chrM 7 8 35.0 35.0 +chrM 8 9 35.0 35.0 +chrM 9 10 35.0 35.0 +chrM 10 11 35.0 35.0 +chrM 11 12 35.0 35.0 +chrM 12 13 35.0 35.0 +chrM 13 14 35.0 35.0 +chrM 14 15 35.0 35.0 +chrM 15 16 35.0 35.0 +chrM 16 17 35.0 35.0 +chrM 17 18 35.0 35.0 +chrM 18 19 35.0 35.0 +chrM 19 20 35.0 35.0 +chrM 20 21 35.0 35.0 +chrM 21 22 35.0 35.0 +chrM 22 23 35.0 35.0 +chrM 23 24 35.0 35.0 +chrM 24 25 35.0 35.0 +chrM 25 26 35.0 35.0 +chrM 26 27 35.0 35.0 +chrM 27 28 35.0 35.0 +chrM 28 29 35.0 35.0 +chrM 29 30 35.0 35.0 +chrM 30 31 35.0 35.0 +chrM 31 32 35.0 35.0 +chrM 32 33 35.0 35.0 +chrM 33 34 35.0 35.0 +chrM 34 35 35.0 35.0 +chrM 35 36 35.0 35.0 +chrM 36 37 35.0 35.0 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotEnrichment_output.txt Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,5 @@ +file featureType percent +bowtie2 test1.bam down 100.00 +bowtie2 test1.bam up 100.00 +bowtie2 test1.bam down 100.00 +bowtie2 test1.bam up 100.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotFingerprint_quality_metrics.tabular Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,3 @@ +Sample AUC Synthetic AUC X-intercept Synthetic X-intercept Elbow Point Synthetic Elbow Point JS Distance Synthetic JS Distance % genome enriched diff. enrichment CHANCE divergence +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269861238192 NA NA NA +bowtie2 test1.bam 0.00493632029864 0.481650684758 0.984443061605 1.15310443503e-24 0.984940883634 0.523268829811 NA 0.269861238192 NA NA NA
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plotPCA_result2.tabular Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,3 @@ +Component bowtie2-test1.bam bowtie2-test1.bam Eigenvalue +1 -0.707106781187 -0.707106781187 6.0 +2 -0.707106781187 0.707106781187 1.23259516441e-32
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/profiler_result2.tabular Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,3 @@ +bin labels -0.0Kb 0.0Kb +bins 1 2 +file_0 genes 2477942.34473 2610259.65234
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/deepTools_seqs.loc.sample Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,27 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of 2bit genome files for use with deepTools. You will +#need to supply these files and then create a deepTools_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The deepTools_seqs.loc +#file has this format: +# +#<unique_build_id> <display_name> <file_path> +# +#So, for example, if your deepTools_seqs.loc began like this: +# +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +# +#then your /depot/data2/galaxy/twobit/ directory +#would need to contain the following 2bit files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit +# +#Your deepTools_seqs.loc file should include an entry per line for +#each file you have stored that you want to be available. Note that +#your files should all have the extension '2bit'. +# +#Please note that the <unique_build_id> is also used as "Species name abbreviation".
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/lastz_seqs.loc.sample Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of 2bit genome files for use with deepTools. +#This file is named lastz_seqs.loc file to make use of an already existing loc +#file from the lastz tool that is created by the twobit data-manager. +#You will need to supply these files and then create a lastz_seqs.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The lastz_seqs.loc +#file has this format: +# +#<unique_build_id> <display_name> <file_path> +# +#So, for example, if your lastz_seqs.loc began like this: +# +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +# +#then your /depot/data2/galaxy/twobit/ directory +#would need to contain the following 2bit files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit +# +#Your lastz_seqs.loc file should include an entry per line for +#each file you have stored that you want to be available. Note that +#your files should all have the extension '2bit'. +# +#Please note that the <unique_build_id> is also used as "Species name abbreviation".
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of 2bit sequence files for use in Lastz --> + <table name="lastz_seqs" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/lastz_seqs.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Dec 05 08:09:05 2016 -0500 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="python" version="2.7.10"> + <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="deeptools" version="2.4.1"> + <repository changeset_revision="e9855a43ac53" name="package_python_2_7_deeptools_2_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>