Mercurial > repos > bgruening > deeptools
changeset 65:9bee2c86eeb1 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
| author | iuc |
|---|---|
| date | Mon, 25 May 2015 05:16:10 -0400 |
| parents | 627004611e98 |
| children | 1dbd76a58d8b |
| files | bamCompare.xml bamCorrelate.xml bamCoverage.xml bamFingerprint.xml bamPEFragmentSize.xml bigwigCompare.xml bigwigCorrelate.xml computeGCBias.xml computeMatrix.xml correctGCBias.xml deepTools_macros.xml heatmapper.xml plotCorrelation.xml profiler.xml test-data/bamCoverage_result1.bw test-data/bamCoverage_result2.bw test-data/bamCoverage_result3.bg test-data/bamCoverage_result4.bg test-data/bamCoverage_result4.bw test-data/correctGCBias_result1.bam test-data/heatmapper_result1.png test-data/profiler_result1.png tool_dependencies.xml |
| diffstat | 22 files changed, 912 insertions(+), 678 deletions(-) [+] |
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--- a/bamCompare.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/bamCompare.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_bamCompare" name="bamCompare" version="@WRAPPER_VERSION@.0"> <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <token name="@BINARY@">bamCompare</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> <![CDATA[ bamCompare @@ -71,7 +70,9 @@ #if str($advancedOpt.ignoreForNormalization).strip() != '': --ignoreForNormalization '$advancedOpt.ignoreForNormalization' #end if - + #if $samFlag: + --samFlag $samFlag + #end if #end if ]]> </command> @@ -157,6 +158,7 @@ <param name="ignoreForNormalization" type="text" value="" size="50" label="regions that should be excluded for calculating the scaling factor" help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" /> + <expand macro="samFlag" /> </when> </conditional> </inputs>
--- a/bamCorrelate.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/bamCorrelate.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="@WRAPPER_VERSION@.0"> <description>correlates pairs of BAM files</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <token name="@BINARY@">bamCorrelate</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> <![CDATA[ #set files=[] @@ -19,8 +18,8 @@ @THREADS@ - --bamfiles #echo " ".join($files) - --labels #echo " ".join($labels) + --bamfiles '#echo "' '".join($files)#' + --labels '#echo "' '".join($labels)#' --fragmentLength $fragmentLength --corMethod $corMethod @@ -29,7 +28,7 @@ #if $output.showOutputSettings == "yes" --outRawCounts '$outFileRawCounts' --outFileCorMatrix '$outFileCorMatrix' - --plotFileFormat $output.outFileFormat + --plotFileFormat '$output.outFileFormat' #else: --plotFileFormat 'png' #end if @@ -38,7 +37,6 @@ --binSize '$mode.binSize' --distanceBetweenBins '$mode.distanceBetweenBins' $mode.doNotRemoveOutliers - #else: --BED $mode.region_file #end if @@ -48,6 +46,10 @@ --region '$mode.region' #end if + #if $plotTitle and str($plotTitle).strip() != "": + --plotTitle '$plotTitle' + #end if + $plotNumbers #if $mode.advancedOpt.showAdvancedOpt == "yes": $mode.advancedOpt.doNotExtendPairedEnds @@ -75,7 +77,10 @@ <param name="fragmentLength" type="integer" value="200" min="1" label="Length of the average fragment size" - help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length. (--fragmentLength)"/> + help ="Reads will be extended to match this length unless they are paired-end, + in which case they will be extended to match the fragment length. + *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will + be extended to match the fragment length. (--fragmentLength)"/> <param name="corMethod" type="select" label="Correlation method"> <option value="spearman" selected="True">Spearman</option> @@ -84,14 +89,18 @@ <conditional name="mode"> <param name="modeOpt" type="select" label="Choose computation mode" - help="In the bins mode, the correlation is computed based on equal length bins. In the BED file mode, as list of genomic regions in BED format has to be given. For each region in the BED file the number of overlapping reads is counted in each of the BAM files. Then the correlation is computed."> + help="In the bins mode, the correlation is computed based on equal + length bins. In the BED file mode, as list of genomic regions in BED + format has to be given. For each region in the BED file the number of + overlapping reads is counted in each of the BAM files. + Then the correlation is computed."> <option value="bins" selected="true">Bins</option> <option value="BED-file">Limit correlation to certain regions (BED file)</option> </param> <when value="bins"> <param name="binSize" type="integer" value="10000" min="1" label="Bin size in bp" - help="Length in base pairs for a window used to sample the genome."/> + help="Length in base pairs for a window used to sample the genome. (--binSize)"/> <param name="distanceBetweenBins" type="integer" value="0" min="0" label="Distance between bins" @@ -99,7 +108,7 @@ the specified 'Bin size'. However, to reduce the computation time, a larger distance between bins can by given. Larger distances result in less bins being - considered"/> + considered. (--distanceBetweenBins)"/> <param name="doNotRemoveOutliers" type="boolean" truevalue="--doNotRemoveOutliers" falsevalue="" label="Do not filter outliers" @@ -113,7 +122,7 @@ bamCorrelate tries to remove outliers using the median absolute deviation (MAD) method applying a threshold of 200 to only consider extremely large - deviations from the median."/> + deviations from the median. (--doNotRemoveOutliers)"/> <expand macro="bamCorrelate_mode_actions" /> </when> @@ -124,7 +133,8 @@ <expand macro="bamCorrelate_mode_actions" /> </when> </conditional> - + <expand macro="plotTitle" /> + <expand macro="plotNumbers" /> <conditional name="output"> <param name="showOutputSettings" type="select" label="Show advanced output settings" > <option value="no" selected="true">no</option> @@ -162,9 +172,11 @@ <test> <repeat name="input_files"> <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> + <param name="label" value="first BAM file" /> </repeat> <repeat name="input_files"> <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> + <param name="label" value="second BAM file" /> </repeat> <param name="modeOpt" value="bins" /> <param name="binSize" value="10" />
--- a/bamCoverage.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/bamCoverage.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_bamCoverage" name="bamCoverage" version="@WRAPPER_VERSION@.0"> <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <token name="@BINARY@">bamCoverage</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> <![CDATA[ bamCoverage @@ -53,7 +52,9 @@ ##if str($advancedOpt.ignoreForNormalization).strip() != '': ## --ignoreForNormalization $advancedOpt.ignoreForNormalization ##end if - + #if $samFlag: + --samFlag $samFlag + #end if #end if ]]> </command> @@ -109,9 +110,8 @@ <expand macro="doNotExtendPairedEnds" /> <expand macro="ignoreDuplicates" /> <expand macro="minMappingQuality" /> - <expand macro="missingDataAsZero" /> - + <expand macro="samFlag" /> <!-- <param name="ignoreForNormalization" type="text" value="" size="50" label="regions that should be excluded for calculating the scaling factor" help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
--- a/bamFingerprint.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/bamFingerprint.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0"> <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <token name="@BINARY@">bamFingerprint</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> <![CDATA[ @multiple_input_bams@ @@ -19,8 +18,7 @@ --fragmentLength $fragmentLength - #set newoutFileName=str($outFileName)+".png" - --plotFile $newoutFileName + --plotFile $outFileName #if $output.showOutputSettings == "yes" --plotFileFormat $output.outFileFormat @@ -46,9 +44,12 @@ #if $advancedOpt.minMappingQuality: --minMappingQuality '$advancedOpt.minMappingQuality' #end if + + #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": + --plotTitle '$advancedOpt.plotTitle' + #end if + #end if - ; mv $newoutFileName $outFileName - ; rm $temp_dir -rf ]]> </command> @@ -74,7 +75,7 @@ <expand macro="ignoreDuplicates" /> <expand macro="minMappingQuality" /> <expand macro="skipZeros" /> - + <expand macro="plotTitle" /> </when> </conditional> <conditional name="output"> @@ -85,7 +86,7 @@ <when value="no" /> <when value="yes"> <expand macro="input_image_file_format" /> - <param name="saveRawCounts" type="boolean" label="Save the bin counts"/> + <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/> </when> </conditional> </inputs>
--- a/bamPEFragmentSize.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/bamPEFragmentSize.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0"> - <description>Given a BAM file it samples several regions to estimate the paird-end fragment length</description> - <expand macro="requirements" /> - <expand macro="stdio" /> + <description>Given a BAM file it samples several regions to estimate the paired-end fragment length</description> <macros> <token name="@BINARY@">bamPEFragmentSize</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> <![CDATA[ bamPEFragmentSize @@ -16,8 +15,6 @@ #end if '$bamInput' > $outfile - && - mv ./hist.png $histogram_outfile ]]> </command> <inputs> @@ -29,7 +26,7 @@ </inputs> <outputs> <data name="outfile" format="txt"/> - <data name="histogram_outfile" format="png"> + <data name="histogram_outfile" from_work_dir="hist.png" format="png"> <filter>histogram is True</filter> </data> </outputs>
--- a/bigwigCompare.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/bigwigCompare.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="@WRAPPER_VERSION@.0"> <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description> - <expand macro="requirements"/> - <expand macro="stdio" /> <macros> <token name="@BINARY@">bigwigCompare</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements"/> <command> <![CDATA[ bigwigCompare @@ -34,6 +33,10 @@ --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2' --binSize $advancedOpt.binSize + #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": + --plotTitle '$advancedOpt.plotTitle' + #end if + #end if ]]> </command> @@ -80,8 +83,17 @@ help="Size of the bins in bp for the output of the bigwig/bedgraph file. (--binSize)"/> <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True" label ="Treat missing data as zero" - help ="This parameter determines if missing data should be replaced with a zero. If set to "no", missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage. (--missingDataAsZero)" /> + help ="This parameter determines if missing data should be replaced with a zero. + If set to "no", missing data will be ignored and will not be included in the + output file at all. Missing data is defined as those regions for which no value exists in + *any* of the bigwig files. The decision to include or exclude missing data depends on + the interpretation of the data. Missing data in a bigwig file may mean that there is no + information available for certain regions, for example a repetitive region that is not + being considered. In the same file regions with low coverage may get zero read counts. + If missing data is replaced by zero, this would convert the excluded repetitive regions + into regions of low coverage. (--missingDataAsZero)" /> <expand macro="scaleFactor" /> + <expand macro="plotTitle" /> </when> </conditional> </inputs>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwigCorrelate.xml Mon May 25 05:16:10 2015 -0400 @@ -0,0 +1,183 @@ +<tool id="deeptools_bamCorrelate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0"> + <description>correlates pairs of BigWig files</description> + <macros> + <token name="@BINARY@">bigwigCorrelate</token> + <import>deepTools_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> +<![CDATA[ + #set files=[] + #set labels=[] + + @multiple_input_bigwigs@ + + bigwigCorrelate + + $mode.modeOpt + + @THREADS@ + + --bwfiles '#echo "' '".join($files)#' + --labels '#echo "' '".join($labels)#' + #if $filterPercentile: + --filterPercentile $filterPercentile + #end if + --corMethod $corMethod + + --plotFile $outFileName + + #if $output.showOutputSettings == "yes" + --outRawCounts '$outFileRawCounts' + --outFileCorMatrix '$outFileCorMatrix' + --plotFileFormat '$output.outFileFormat' + #else: + --plotFileFormat 'png' + #end if + + #if $mode.modeOpt == "bins": + --binSize '$mode.binSize' + #else: + --BED $mode.region_file + #end if + + #### options available in both modes + #if str($region.value) != '': + --region '$region' + #end if + + #if $advancedOpt.showAdvancedOpt == "yes": + + $advancedOpt.includeZeros + + #if $advancedOpt.zMin: + --zMin $advancedOpt.zMin + #end if + #if $advancedOpt.zMax: + --zMax $advancedOpt.zMax + #end if + --colorMap '$advancedOpt.colorMap' + + #if $plotTitle and str($plotTitle).strip() != "": + --plotTitle '$plotTitle' + #end if + $plotNumbers + + #end if +]]> + </command> + + <inputs> + <expand macro="multiple_input_bigwigs" /> + + <param name="filterPercentile" type="float" optional="True" value="" min="0.0" max="100.0" + label="Percentile used to filter out extreme outliers" + help ="If not specified, it is automatically set to 99.9 in analyses + using Pearson correlation! This means that values + above that threshold, which consistently occur in all + datasets, will not be taken into account for the + correlation analysis. This behavior can be overridden + by a user specified value from within the 0.0 to 100.0 + range. (--filterPercentile)"/> + + <param name="corMethod" type="select" label="Correlation method" help="(--corMethod)"> + <option value="spearman" selected="True">Spearman</option> + <option value="pearson">Pearson</option> + </param> + + <conditional name="mode"> + <param name="modeOpt" type="select" label="Choose computation mode" + help="In the bins mode, the correlation is computed based on equal length bins. + In the BED file mode, as list of genomic regions in BED format has to be given. + For each region in the BED file the number of overlapping reads is counted in + each of the BAM files. Then the correlation is computed."> + <option value="bins" selected="true">Bins</option> + <option value="BED-file">Limit correlation to certain regions (BED file)</option> + </param> + <when value="bins"> + <param name="binSize" type="integer" value="10000" min="1" + label="Bin size in bp" + help="Length in base pairs for a window used to sample the genome. (--binSize)"/> + </when> + <when value="BED-file"> + <param name="region_file" type="data" format="bed" + label="Region file in BED format" + help="Correlation is computed for the number of reads that overlap such regions."/> + </when> + </conditional> + + <expand macro="bigwigCorrelate_mode_actions" /> + <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"> + <expand macro="input_image_file_format"/> + <param name="saveRawCounts" type="boolean" label="Save the bin counts"/> + <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/> + </when> + </conditional> + + </inputs> + <outputs> + <expand macro="output_image_file_format" /> + <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveRawCounts'] is True + )) + </filter> + </data> + <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix"> + <filter> + (( + output['showOutputSettings'] == 'yes' and + output['saveCorMatrix'] is True + )) + </filter> + </data> + </outputs> + <tests> + <test> + <repeat name="input_files"> + <param name="bigwigfile" value="1.bigwig" ftype="bigwig" /> + <param name="label" value="first bigwig file" /> + </repeat> + <repeat name="input_files"> + <param name="bigwigfile" value="1.bigwig" ftype="bigwig" /> + <param name="label" value="second bigwig file" /> + </repeat> + <param name="modeOpt" value="bins" /> + <param name="binSize" value="10" /> + <param name="showOutputSettings" value="no" /> + <output name="outFileName" file="bigwigCorrelate_result1.png" ftype="png" compare="sim_size" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +bigwigCorrelate computes the overall similarity between two or more bigWig +files based on coverage means of genomic regions. The correlation analysis +is performed for the entire genome by running the program in 'bins' mode, +or for certain regions only in 'BED-file' mode. Pearson or Spearman analyses +are available to compute correlation coefficients. Results are saved to a +heat map file. Further output files are optional. + + +**Output files**: + +- **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation +- data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used + + +----- + +@REFERENCES@ +]]> + </help> + <expand macro="citations" /> +</tool>
--- a/computeGCBias.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/computeGCBias.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_computeGCBias" name="computeGCBias" version="@WRAPPER_VERSION@.0"> <description>to see whether your samples should be normalized for GC bias</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <token name="@BINARY@">computeGCBias</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> <![CDATA[ ln -s $bamInput local_bamInput.bam; @@ -31,7 +30,6 @@ #end if #if $advancedOpt.showAdvancedOpt == "yes": - --sampleSize '$advancedOpt.sampleSize' --regionSize '$advancedOpt.regionSize' @@ -70,10 +68,17 @@ label="Number of sampling points to be considered" help="(--sampleSize)" /> <param name="regionSize" type="integer" value="300" min="1" label="Region size" - help ="To plot the reads per GC over a region, the size of the region is required (see below for more details of the mthod). By default, the bin size is set to 300 bp, which is close to the standard fragment size many sequencing applications. However, if the depth of sequencing is low, a larger bin size will be required, otherwise many bins will not overlap with any read. (--regionSize)"/> + help ="To plot the reads per GC over a region, the size of the region is + required (see below for more details of the mthod). By default, the bin size + is set to 300 bp, which is close to the standard fragment size many sequencing + applications. However, if the depth of sequencing is low, a larger bin size will + be required, otherwise many bins will not overlap with any read. (--regionSize)"/> <param name="filterOut" type="data" format="bed" optional="true" label="BED file containing genomic regions to be excluded from the estimation of the correction" - help="Such regions usually contain repetitive regions and peaks that if included will bias the correction. It is recommended to filter out known repetitive regions if multi-reads (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" /> + help="Such regions usually contain repetitive regions and peaks that if included will + bias the correction. It is recommended to filter out known repetitive regions if multi-reads + (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, + it is recommended to first use a peak caller to identify and filter out the identified peaks. (--filterOut)" /> <param name="extraSampling" type="data" format="bed" optional="true" label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome" help="(--extraSampling)" />
--- a/computeMatrix.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/computeMatrix.xml Mon May 25 05:16:10 2015 -0400 @@ -1,32 +1,27 @@ <tool id="deeptools_computeMatrix" name="computeMatrix" version="@WRAPPER_VERSION@.0"> - <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description> - <expand macro="requirements" /> - <expand macro="stdio" /> + <description>preparation step to plot a heatmap or a profile</description> <macros> <token name="@BINARY@">computeMatrix</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> <![CDATA[ #import tempfile - #set $temp_input_handle = tempfile.NamedTemporaryFile() - #set $temp_input_path = $temp_input_handle.name - #silent $temp_input_handle.close() - #for $rf in $regionsFiles: - cat "$rf.regionsFile" >> $temp_input_path; + cat "$rf.regionsFile" >> ./temp_input_path; #if str($rf.label.value).strip(): - echo "\#$rf.label.value" >> $temp_input_path; + echo "\#$rf.label.value" >> ./temp_input_path; #else: - echo "\#$rf.regionsFile.name" >> $temp_input_path; + echo "\#$rf.regionsFile.name" >> ./temp_input_path; #end if #end for computeMatrix $mode.mode_select - --regionsFileName '$temp_input_path' + --regionsFileName ./temp_input_path --scoreFileName '$scoreFile' --outFileName '$outFileName' @@ -79,24 +74,33 @@ #end if #end if - ; rm $temp_input_path ]]> </command> <inputs> <repeat name="regionsFiles" title="regions to plot" min="1"> - <param name="regionsFile" format="bed" type="data" label="Regions to plot" help="File, in BED format, containing the regions to plot."/> - <param name="label" type="text" size="30" optional="true" value="" label="Label" help="Label to use in the output."/> + <param name="regionsFile" format="bed" type="data" label="Regions to plot" + help="File, in BED format, containing the regions to plot."/> + <param name="label" type="text" size="30" optional="true" value="" label="Label" + help="Label to use in the output."/> </repeat> <param name="scoreFile" format="bigwig" type="data" label="Score file" - help="Should be a bigWig file (containing a score, usually covering the whole genome). You can generate a bigWig file either from a bedGraph or WIG file using UCSC tools or from a BAM file using the deepTool bamCoverage. (-scoreFile)"/> + help="Should be a bigWig file (containing a score, usually covering + the whole genome). You can generate a bigWig file either from a + bedGraph or WIG file using UCSC tools or from a BAM file using the + deepTool bamCoverage. (-scoreFile)"/> <conditional name="mode" > <param name="mode_select" type="select" label="computeMatrix has two main output options" - help="In the scale-regions mode, all regions in the BED file are stretched or shrunk to the same length (bp) that is indicated by the user. Reference-point refers to a position within the BED regions (e.g start of region). In the reference-point mode only those genomic positions before (downstream) and/or after (upstream) the reference point will be plotted."> + help="In the scale-regions mode, all regions in the BED file are + stretched or shrunk to the same length (bp) that is indicated + by the user. Reference-point refers to a position within the BED + regions (e.g start of region). In the reference-point mode only + those genomic positions before (downstream) and/or after (upstream) + the reference point will be plotted."> <option value="scale-regions" selected="true">scale-regions</option> <option value="reference-point">reference-point</option> </param> @@ -106,7 +110,9 @@ label="Distance in bp to which all regions are going to be fitted" help="(--regionBodyLength)"/> <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" - help ="Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. "peak start". (--startLabel)" /> + help ="Label shown in the plot for the start of the region. + Default is TSS (transcription start site), but could be changed to anything, + e.g. "peak start". (--startLabel)" /> <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="Label shown in the plot for the region end. Default is TES (transcription end site). (--endLabel)"/> @@ -119,10 +125,12 @@ <when value="yes"> <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" - help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/> + help="If the regions are genes, this would be the + distance upstream of the transcription start site. (--beforeRegionStartLength)"/> <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" - help="If the regions are genes, this would be the distance downstream of the transcription end site. (--afterRegionStartLength)"/> + help="If the regions are genes, this would be the + distance downstream of the transcription end site. (--afterRegionStartLength)"/> </when> </conditional> </when> @@ -134,7 +142,8 @@ </param> <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" - help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/> + help="This is useful to visualize the region end when not using the + scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/> <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/> @@ -188,23 +197,33 @@ <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" label="Indicate missing data as zero" - help="Set to "yes", if missing data should be indicated as zeros. Default is to ignore such cases which will be depicted as black areas in the heatmap. (see "Missing data color" options of the heatmapper for additional options). (--missingDataAsZero)"/> + help="Set to "yes", if missing data should be indicated as zeros. + Default is to ignore such cases which will be depicted as black areas in the + heatmap. (see "Missing data color" options of the heatmapper for additional options). + (--missingDataAsZero)"/> <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label="Skip zeros" - help="Whether regions with only scores of zero should be included or not. Default is to include them. (--skipZeros)"/> + help="Whether regions with only scores of zero should be included or not. + Default is to include them. (--skipZeros)"/> <param name="minThreshold" type="float" optional="True" label="Minimum threshold" - help="Any region containing a value that is equal or less than this numeric value will be skipped. This is useful to skip, for example, genes where the read count is zero for any of the bins. This could be the result of unmappable areas and can bias the overall results. (--minThreshold)"/> + help="Any region containing a value that is equal or less than this numeric + value will be skipped. This is useful to skip, for example, genes where the + read count is zero for any of the bins. This could be the result of + unmappable areas and can bias the overall results. (--minThreshold)"/> <param name="maxThreshold" type="float" optional="True" label="Maximum threshold" - help="Any region containing a value that is equal or higher that this numeric value will be skipped. The max threshold is useful to skip those few regions with very high read counts (e.g. major satellites) that may bias the average values. (--maxThreshold)"/> + help="Any region containing a value that is equal or higher that this + numeric value will be skipped. The max threshold is useful to skip those + few regions with very high read counts (e.g. major satellites) that may + bias the average values. (--maxThreshold)"/> <param name="scale" type="float" optional="True" label="Scaling factor" help="If set, all values are multiplied by this number. (--scale)"/> </when> </conditional> </inputs> <outputs> - <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> + <data format="deeptools_matrix" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> <expand macro="output_graphic_outputs" /> <expand macro="output_save_matrix_values" /> </outputs> @@ -223,7 +242,7 @@ <param name="missingDataAsZero" value="True" /> <param name="beforeRegionStartLength" value="10" /> <param name="afterRegionStartLength" value="10" /> - <output name="outFileName" file="computeMatrix_result1.gz" ftype="bgzip" compare="sim_size" /> + <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_matrix" compare="sim_size" /> </test> <test> <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> @@ -233,7 +252,7 @@ <param name="binSize" value="10" /> <param name="beforeRegionStartLength" value="10" /> <param name="afterRegionStartLength" value="10" /> - <output name="outFileName" file="computeMatrix_result2.gz" ftype="bgzip" compare="sim_size" /> + <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_matrix" compare="sim_size" /> </test> </tests> <help>
--- a/correctGCBias.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/correctGCBias.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_correctGCBias" name="correctGCBias" version="@WRAPPER_VERSION@.0"> <description>uses the output from computeGCBias to generate corrected BAM files</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <token name="@BINARY@">correctGCBias</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> <![CDATA[ ln -s $bamInput local_bamInput.bam; @@ -33,7 +32,7 @@ <inputs> <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" /> <param name="bamInput" format="bam" type="data" - label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/> + label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted. (--bamfile)" /> <expand macro="reference_genome_source" /> <expand macro="effectiveGenomeSize" /> <expand macro="region_limit_operation" />
--- a/deepTools_macros.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/deepTools_macros.xml Mon May 25 05:16:10 2015 -0400 @@ -13,23 +13,53 @@ <expand macro="doNotExtendPairedEnds" /> <expand macro="ignoreDuplicates" /> <expand macro="minMappingQuality" /> - <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" - label="Include zeros" - help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" /> - <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities" - help="If not specified the value is set automatically. (--zMin)"/> - <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities" - help="If not specified the value is set automatically. (--zMax)"/> + <expand macro="includeZeros" /> + <expand macro="zMin_zMax" /> <expand macro="colormap" /> </when> </conditional> </xml> + + <xml name="bigwigCorrelate_mode_actions"> + + <expand macro="region_limit_operation" /> + + <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"> + <expand macro="includeZeros" /> + <expand macro="zMin_zMax" /> + <expand macro="colormap" /> + <expand macro="plotTitle" /> + <expand macro="plotNumbers" /> + </when> + </conditional> + </xml> + + + <xml name="includeZeros"> + <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" + label="Include zeros" + help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" /> + </xml> + <xml name="zMin_zMax"> + <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities" + help="If not specified the value is set automatically. (--zMin)"/> + <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities" + help="If not specified the value is set automatically. (--zMax)"/> + </xml> + <xml name="region_limit_operation"> <param name="region" type="text" value="" label="Region of the genome to limit the operation to" help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000". (--region)" /> </xml> + <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> <token name="@WRAPPER_VERSION@">1.5.9.2</token> <xml name="requirements"> @@ -39,6 +69,7 @@ <requirement type="package" version="1.5.9">deepTools</requirement> <yield /> </requirements> + <expand macro="stdio" /> <version_command>@BINARY@ --version</version_command> </xml> @@ -77,6 +108,16 @@ #end if </token> + <xml name="samFlag"> + <param name="samFlag" type="integer" optional="true" value="" + label="Filter 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. (--samFlag)"/> + </xml> + <xml name="plotNumbers"> + <param name="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. (--plotNumbers)"/> + </xml> <xml name="doNotExtendPairedEnds"> <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" label="Do not extend paired ends" @@ -141,11 +182,6 @@ .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de .. _help site: https://github.com/fidelram/deepTools/wiki/ -**References** - -If you use this Galaxy tool in work leading to a scientific publication please -cite the following paper: - </token> <xml name="citations"> <citations> @@ -162,7 +198,24 @@ <param name="label" type="text" size="30" optional="true" value="" label="Label" help="Label to use in the output. If not given the dataset name will be used instead."/> - </repeat> + </repeat> + </xml> + + <xml name="multiple_input_bigwigs"> + <repeat name="input_files" title="BigWig files" min="2"> + <param name="bigwigfile" type="data" format="bigwig" + label="Bigwig file" + help="The Bigwig file must be sorted."/> + <param name="label" type="text" size="30" optional="true" value="" + label="Label" + help="Label to use in the output. If not given the dataset name will be used instead."/> + </repeat> + </xml> + + <xml name="plotTitle"> + <param name="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. (--plotTitle)" /> </xml> <token name="@multiple_input_bams@"> @@ -187,6 +240,27 @@ #end for </token> + <token name="@multiple_input_bigwigs@"> + #import tempfile + #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + #set files=[] + #set labels=[] + #for $i in $input_files: + #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) + #set $temp_input_path = $temp_input_handle.name + #silent $temp_input_handle.close() + #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) + #silent $files.append('%s.bw' % $temp_input_path) + + ##set $files += [str($i.bigwigfile)] + #if str($i.label.value) != "": + #set $labels += ["\"%s\"" % ($i.label.value)] + #else + #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] + #end if + #end for + </token> + <xml name="reference_genome_source"> <conditional name="source"> <param name="ref_source" type="select" label="Reference genome">
--- a/heatmapper.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/heatmapper.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0"> <description>creates a heatmap for a score associated to genomic regions</description> - <expand macro="requirements"/> - <expand macro="stdio" /> <macros> <token name="@BINARY@">heatmapper</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements"/> <command> <![CDATA[ heatmapper @@ -76,7 +75,7 @@ --refPointLabel '$advancedOpt.referencePointLabel' --regionsLabel '$advancedOpt.regionsLabel' - #if str($advancedOpt.plotTitle.value) != "None": + #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": --plotTitle '$advancedOpt.plotTitle' #end if @@ -177,8 +176,7 @@ </valid> </sanitizer> </param> - <param name="plotTitle" type="text" value="" size="30" - label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title. (--plotTitle)" /> + <expand macro="plotTitle" /> <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/> @@ -194,7 +192,7 @@ </outputs> <tests> <test> - <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" /> + <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" /> <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" /> </test> </tests>
--- a/plotCorrelation.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/plotCorrelation.xml Mon May 25 05:16:10 2015 -0400 @@ -1,11 +1,10 @@ <tool id="deeptools_plotCorrelation" name="plotCorrelation" version="@WRAPPER_VERSION@.0"> <description>creates a heatmap for a score associated to genomic regions</description> - <expand macro="requirements"/> - <expand macro="stdio" /> <macros> <token name="@BINARY@">heatmapper</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements"/> <command> <![CDATA[ heatmapper @@ -76,7 +75,7 @@ --refPointLabel '$advancedOpt.referencePointLabel' --regionsLabel '$advancedOpt.regionsLabel' - #if str($advancedOpt.plotTitle.value) != "None": + #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": --plotTitle '$advancedOpt.plotTitle' #end if @@ -110,13 +109,6 @@ <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values"/> - <param name="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. (--plotNumbers)"/> - - - - <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/> <param name="yMax" type="float" value="" size="3" @@ -142,27 +134,33 @@ <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" - help ="[only for scale-regions mode] Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. "peak start"." /> + help ="[only for scale-regions mode] Label shown in the plot for the start of the region. + Default is TSS (transcription start site), but could be changed to anything, e.g. "peak start". (--startLabel)" /> <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" - help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/> + help="[only for scale-regions mode] Label shown in the plot for the region end. (--endLabel)"/> <param name="referencePointLabel" type="text" value="TSS" size="10" label="Reference point label" - help ="[only for scale-regions mode] Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. "peak start" etc." /> + help ="[only for scale-regions mode] Label shown in the plot for the reference-point. + Default is the same as the reference point selected (e.g. TSS), + but could be anything, e.g. "peak start" etc (--referencePointLabel)" /> <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" - help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2."> + help="If more than one region is being plotted a list of labels + separated by comma and limited by quotes, is required. For example, label1, label2. (--regionsLabel)"> <sanitizer> <valid initial="string.printable"> </valid> </sanitizer> </param> - <param name="plotTitle" type="text" value="" size="30" - label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title. (--plotTitle)" /> - <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" - label="Do one plot per group" - help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/> + + <expand macro="plotTitle" /> + <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" + label="Do one plot per group" + help="When computeMatrix was used on more than one group of genes, + the average plots for all the groups will be drawn in one panel by default. + If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/> <expand macro="kmeans_clustering" /> </when>
--- a/profiler.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/profiler.xml Mon May 25 05:16:10 2015 -0400 @@ -2,12 +2,11 @@ <description> creates a profile plot for a score associated to genomic regions </description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <token name="@BINARY@">profiler</token> <import>deepTools_macros.xml</import> </macros> + <expand macro="requirements" /> <command> <![CDATA[ profiler @@ -44,7 +43,7 @@ --regionsLabel '$advancedOpt.regionsLabel' - #if str($advancedOpt.plotTitle).strip() != "": + #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "": --plotTitle '$advancedOpt.plotTitle' #end if @@ -82,7 +81,9 @@ <when value="yes"> <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" - help ="[only for scale-regions mode] Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. "peak start"." /> + help ="[only for scale-regions mode] Label shown in the plot + for the start of the region. Default is TSS (transcription start site), + but could be changed to anything, e.g. "peak start"." /> <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/> @@ -115,7 +116,14 @@ label="Plot width" help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." /> <param name="plotType" type="select" label="Plot type" - help="For the summary plot (profile) only. The "lines" option will plot the profile line based on the average type selected. The "fill" option fills the region between zero and the profile curve. The fill in color is semi transparent to distinguish different profiles. The "add standard error" option colors the region between the profile and the standard error of the data. As in the case of fill, a semi-transparent color is used. The option "overlapped_lines" plots each region values, one on top of the other; this option only works if "one plot per proup" is set."> + help="For the summary plot (profile) only. The "lines" option will + plot the profile line based on the average type selected. The "fill" + option fills the region between zero and the profile curve. The fill in color is + semi transparent to distinguish different profiles. The "add standard error" + option colors the region between the profile and the standard error of the data. + As in the case of fill, a semi-transparent color is used. + The option "overlapped_lines" plots each region values, one on top of + the other; this option only works if "one plot per proup" is set."> <option value="lines" selected="true">lines</option> <option value="fill">fill</option> <option value="se">add standard error</option> @@ -123,20 +131,23 @@ </param> <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" - help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, "label1, label2"."/> - <param name="plotTitle" type="text" value="" size="30" - label="Title of the plot" - help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." /> + help="If more than one region is being plotted a list of labels separated + by comma and limited by quotes, is required. For example, "label1, label2"."/> + + <expand macro="plotTitle" /> <param name="colors" type="text" value="" size="40" label="List of colors to use for the plotted lines" - help="Color names and html hex strings (e.g. #eeff22) are accepted. The color names should be given separated by spaces. (--colors red blue green)"> + help="Color names and html hex strings (e.g. #eeff22) are accepted. + The color names should be given separated by spaces. (--colors red blue green)"> <validator type="expression" message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator> </param> <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" - help="When the region file contains groups separated by "#", the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/> + help="When the region file contains groups separated by "#", the default is + to plot the averages for the distinct plots in one plot. If this option is set, each group + will get its own plot, stacked on top of each other."/> <param name="yMin" type="float" value="" size="3" optional="true" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/> <param name="yMax" type="float" value="" size="3" optional="true" @@ -155,8 +166,15 @@ <expand macro="output_image_file_format" /> <expand macro="output_graphic_outputs" /> </outputs> + <tests> + <test> + <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" /> + <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="100" /> + </test> + </tests> <help> <![CDATA[ + **What it does** This tool plots the average enrichments over all genomic
--- a/test-data/bamCoverage_result3.bg Sun Mar 22 13:02:33 2015 -0400 +++ b/test-data/bamCoverage_result3.bg Mon May 25 05:16:10 2015 -0400 @@ -1,12 +1,11 @@ -chrM 0 210 8173200.00 -chrM 210 220 7999302.13 -chrM 220 230 7129812.77 -chrM 230 240 5564731.91 -chrM 240 250 4173548.94 -chrM 250 260 2434570.21 -chrM 260 300 1912876.60 -chrM 300 16310 1738978.72 -chrM 16310 16320 1565080.85 -chrM 16320 16330 869489.36 -chrM 16330 16340 695591.49 -chrM 16340 16350 347795.74 +chrM 0 210 12259800.00 +chrM 210 220 11998953.19 +chrM 220 230 10694719.15 +chrM 230 240 8347097.87 +chrM 240 250 6260323.40 +chrM 250 260 3391008.51 +chrM 260 16310 2608468.09 +chrM 16310 16320 2347621.28 +chrM 16320 16330 1304234.04 +chrM 16330 16340 1043387.23 +chrM 16340 16350 521693.62
--- a/test-data/bamCoverage_result4.bg Sun Mar 22 13:02:33 2015 -0400 +++ b/test-data/bamCoverage_result4.bg Mon May 25 05:16:10 2015 -0400 @@ -1,456 +1,460 @@ -phiX174 0 10 3742.31 -phiX174 10 20 18711.54 -phiX174 20 70 63619.23 -phiX174 70 90 82330.77 -phiX174 90 100 101042.31 -phiX174 100 120 104784.62 -phiX174 120 140 119753.85 -phiX174 140 160 138465.38 -phiX174 160 170 153434.62 -phiX174 170 180 183373.08 -phiX174 180 200 202084.62 -phiX174 200 210 205826.92 -phiX174 210 220 224538.46 -phiX174 220 230 265703.85 -phiX174 230 240 295642.31 -phiX174 240 250 303126.92 -phiX174 250 260 318096.15 -phiX174 260 270 366746.15 -phiX174 270 280 404169.23 -phiX174 280 290 419138.46 -phiX174 290 310 437850.00 -phiX174 310 320 456561.54 -phiX174 320 330 479015.38 -phiX174 330 350 497726.92 -phiX174 350 360 505211.54 -phiX174 360 370 508953.85 -phiX174 370 380 523923.08 -phiX174 380 400 550119.23 -phiX174 400 410 553861.54 -phiX174 410 420 550119.23 -phiX174 420 430 565088.46 -phiX174 430 440 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--- a/tool_dependencies.xml Sun Mar 22 13:02:33 2015 -0400 +++ b/tool_dependencies.xml Mon May 25 05:16:10 2015 -0400 @@ -1,93 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="samtools" version="0.1.19"> - <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="numpy" version="1.7.1"> - <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="matplotlib" version="1.2.1"> - <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="scipy" version="0.12.0"> - <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="pysam" version="0.7.7"> - <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="bx-python" version="0.7.1"> - <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="ucsc_tools" version="0.1"> - <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="deepTools" version="1.5.10"> + <repository changeset_revision="41de4f005517" name="package_python_2_7_deeptools_1_5_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="deepTools" version="1.5.9"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action> - <action type="set_environment_for_install"> - <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="pysam" version="0.7.7" /> - </repository> - <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="bx-python" version="0.7.1" /> - </repository> - <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="numpy" version="1.7.1" /> - </repository> - <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="matplotlib" version="1.2.1" /> - </repository> - <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="scipy" version="0.12.0" /> - </repository> - <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="samtools" version="0.1.19" /> - </repository> - <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="ucsc_tools" version="0.1" /> - </repository> - </action> - <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command"> - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && - python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin - </action> - - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable> - <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> - <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable> - <!-- include samtools into PATH --> - <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable> - <!-- include numpy --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable> - <!-- include matplotlib --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable> - <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[MATPLOTLIB_LIB_PATH]</environment_variable> - <!-- include scipy --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable> - <!-- include bx-python --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[BX_PYTHON_PATH]/lib/python</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[BX_PYTHON_PATH]/bin</environment_variable> - <!-- include pysam --> - <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYSAM_PATH]/lib/python</environment_variable> - <environment_variable action="prepend_to" name="PATH">$ENV[PYSAM_PATH]/bin</environment_variable> - <!-- include ucsc tools --> - <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable> - - <!-- disable the config file of deepTools --> - <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable> - </action> - </actions> - </install> - <readme> - Installation of deepTools from Fidel Ramirez. - https://github.com/fidelram/deepTools - </readme> - </package> </tool_dependency>