Mercurial > repos > bgruening > deeptools
changeset 52:c0a054f2eff8 draft
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--- a/bamCompare.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/bamCompare.xml Mon Dec 22 18:56:27 2014 -0500 @@ -7,53 +7,54 @@ <import>deepTools_macros.xml</import> </macros> <command> +<![CDATA[ bamCompare @THREADS@ - --bamfile1 '$bamFile1' - -bai1 '${bamFile1.metadata.bam_index}' - --bamfile2 '$bamFile2' - -bai2 '${bamFile2.metadata.bam_index}' + --bamfile1 '$bamFile1' + -bai1 '${bamFile1.metadata.bam_index}' + --bamfile2 '$bamFile2' + -bai2 '${bamFile2.metadata.bam_index}' - --outFileName '$outFileName' - --outFileFormat '$outFileFormat' + --outFileName '$outFileName' + --outFileFormat '$outFileFormat' - --fragmentLength $fragmentLength - --binSize $binSize + --fragmentLength $fragmentLength + --binSize $binSize - #if $scaling.method == 'SES': - --scaleFactorsMethod SES - --sampleLength $scaling.sampleLength - #elif $scaling.method == 'readCount': - --scaleFactorsMethod readCount - #elif $scaling.method == 'own': - --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2' - #end if + #if $scaling.method == 'SES': + --scaleFactorsMethod SES + --sampleLength $scaling.sampleLength + #elif $scaling.method == 'readCount': + --scaleFactorsMethod readCount + #elif $scaling.method == 'own': + --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2' + #end if - --ratio $comparison.type + --ratio $comparison.type - #if $comparison.type=='subtract': - #if $comparison.normalization.type=='rpkm': - --normalizeUsingRPKM - #elif $comparison.normalization.type=='1x': + #if $comparison.type=='subtract': + #if $comparison.normalization.type=='rpkm': + --normalizeUsingRPKM + #elif $comparison.normalization.type=='1x': - #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": - --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize - #else: - --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt - #end if + #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize + #else: + --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt + #end if - #end if - #elif $comparison.type in ['ratio','log2']: - --pseudocount $comparison.pseudocount - #end if + #end if + #elif $comparison.type in ['ratio','log2']: + --pseudocount $comparison.pseudocount + #end if - #if str($region).strip() != '': - --region '$region' - #end if + #if str($region).strip() != '': + --region '$region' + #end if - #if $advancedOpt.showAdvancedOpt == "yes": + #if $advancedOpt.showAdvancedOpt == "yes": #if $advancedOpt.smoothLength: --smoothLength '$advancedOpt.smoothLength' #end if @@ -71,24 +72,21 @@ --ignoreForNormalization $advancedOpt.ignoreForNormalization #end if - #end if - + #end if +]]> </command> - <inputs> <param name="bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)" help="The BAM file must be sorted."/> - <param name="bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)" help="The BAM file must be sorted."/> - - <param name="fragmentLength" type="integer" value="300" min="1" + <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. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see "normalize coverage to 1x"). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> + 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. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see "normalize coverage to 1x"). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * 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="binSize" type="integer" value="50" min="1" label="Bin size in bp" - help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/> + help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. (--binSize)"/> <conditional name="scaling"> <param name="method" type="select" @@ -104,11 +102,7 @@ </when> <when value="readCount" /> <when value="own"> - <param name="scaleFactor1" type="float" value="1" - label="Scale factor for treatment"/> - - <param name="scaleFactor2" type="float" value="1" - label="Scale factor for input"/> + <expand macro="scaleFactor" /> </when> </conditional> @@ -145,9 +139,7 @@ <option value="bigwig" selected="true">bigwig</option> <option value="bedgraph">bedgraph</option> </param> - <expand macro="region_limit_operation" /> - <conditional name="advancedOpt"> <param name="showAdvancedOpt" type="select" label="Show advanced options" > <option value="no" selected="true">no</option> @@ -155,32 +147,18 @@ </param> <when value="no" /> <when value="yes"> - <param name="smoothLength" type="integer" value="1" optional="true" min="1" label="Smooth values using the following length (in bp)" - help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> - - <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" - label="Do not extend paired ends" - help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> - - <param name="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." /> - - <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" - label="Minimum mapping quality (e.g. BOWTIE2 measures)" - help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> - + help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied. (--smoothLength)"/> + <expand macro="doNotExtendPairedEnds" /> + <expand macro="ignoreDuplicates" /> + <expand macro="minMappingQuality" /> <expand macro="missingDataAsZero" /> - <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" /> - </when> </conditional> - </inputs> <outputs> <data format="bigwig" name="outFileName"> @@ -190,8 +168,21 @@ </change_format> </data> </outputs> + <tests> + <test> + <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" /> + <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" /> + <param name="showAdvancedOpt" value="no" /> + <param name="outFileFormat" value="bigwig" /> + <param name="fragmentLength" value="100" /> + <param name="outFileFormat" value="bedgraph" /> + <param name="binSize" value="5" /> + <param name="type" value="ratio" /> + <output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph" /> + </test> + </tests> <help> - +<![CDATA[ **What it does** This tool compares two BAM files based on the number of mapped reads. To @@ -224,7 +215,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/bamCorrelate.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/bamCorrelate.xml Mon Dec 22 18:56:27 2014 -0500 @@ -7,6 +7,7 @@ <import>deepTools_macros.xml</import> </macros> <command> +<![CDATA[ #set files=[] #set labels=[] @@ -66,14 +67,15 @@ --colorMap '$mode.advancedOpt.colorMap' #end if +]]> </command> <inputs> <expand macro="multiple_input_bams" /> - <param name="fragmentLength" type="integer" value="300" min="1" + <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."/> + 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> @@ -116,10 +118,11 @@ <expand macro="bamCorrelate_mode_actions" /> </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."/> + <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."/> <expand macro="bamCorrelate_mode_actions" /> </when> - </conditional> <conditional name="output"> @@ -155,8 +158,22 @@ </filter> </data> </outputs> + <tests> + <test> + <repeat name="input_files"> + <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> + </repeat> + <repeat name="input_files"> + <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> + </repeat> + <param name="modeOpt" value="bins" /> + <param name="binSize" value="10" /> + <param name="showOutputSettings" value="no" /> + <output name="outFileName" file="bamCorrelate_result1.png" ftype="png" compare="sim_size" /> + </test> + </tests> <help> - +<![CDATA[ **What it does** This tool is useful to assess the overall similarity of different BAM files. A typical application @@ -183,7 +200,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/bamCoverage.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/bamCoverage.xml Mon Dec 22 18:56:27 2014 -0500 @@ -7,62 +7,64 @@ <import>deepTools_macros.xml</import> </macros> <command> +<![CDATA[ bamCoverage - @THREADS@ + @THREADS@ - --bam '$bamInput' - --bamIndex ${bamInput.metadata.bam_index} - --outFileName '$outFileName' - --outFileFormat '$outFileFormat' + --bam '$bamInput' + --bamIndex ${bamInput.metadata.bam_index} + --outFileName '$outFileName' + --outFileFormat '$outFileFormat' - --fragmentLength $fragmentLength - --binSize $binSize + --fragmentLength $fragmentLength + --binSize $binSize - #if $scaling.type=='rpkm': - --normalizeUsingRPKM - #elif $scaling.type=='1x': - #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": - --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize - #else: - --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt - #end if - #elif $scaling.type=='own': - --scaleFactor $scaling.scaleFactor - #end if - - #if str($region).strip() != '': - --region '$region' - #end if - - #if $advancedOpt.showAdvancedOpt == "yes": - #if $advancedOpt.smoothLength: - --smoothLength '$advancedOpt.smoothLength' + #if $scaling.type=='rpkm': + --normalizeUsingRPKM + #elif $scaling.type=='1x': + #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize + #else: + --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt + #end if + #elif $scaling.type=='own': + --scaleFactor $scaling.scaleFactor #end if - $advancedOpt.doNotExtendPairedEnds - $advancedOpt.ignoreDuplicates - - #if $advancedOpt.minMappingQuality: - --minMappingQuality '$advancedOpt.minMappingQuality' + #if str($region).strip() != '': + --region '$region' #end if - --missingDataAsZero $advancedOpt.missingDataAsZero + #if $advancedOpt.showAdvancedOpt == "yes": + #if $advancedOpt.smoothLength: + --smoothLength '$advancedOpt.smoothLength' + #end if + + $advancedOpt.doNotExtendPairedEnds + $advancedOpt.ignoreDuplicates - ##if str($advancedOpt.ignoreForNormalization).strip() != '': - ## --ignoreForNormalization $advancedOpt.ignoreForNormalization - ##end if + #if $advancedOpt.minMappingQuality: + --minMappingQuality '$advancedOpt.minMappingQuality' + #end if + + --missingDataAsZero $advancedOpt.missingDataAsZero - #end if + ##if str($advancedOpt.ignoreForNormalization).strip() != '': + ## --ignoreForNormalization $advancedOpt.ignoreForNormalization + ##end if + + #end if +]]> </command> <inputs> <param name="bamInput" format="bam" type="data" label="BAM file" help="The BAM file must be sorted."/> - <param name="fragmentLength" type="integer" value="300" min="1" + <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. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see "normalize coverage to 1x"). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> + 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. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see "normalize coverage to 1x"). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. *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="binSize" type="integer" value="50" min="1" label="Bin size in bp" @@ -102,19 +104,11 @@ <when value="yes"> <param name="smoothLength" type="integer" value="1" optional="true" min="1" label="Smooth values using the following length (in bp)" - help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/> - - <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" - label="Do not extend paired ends" - help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> + help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied. (--smoothLength)"/> - <param name="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." /> - - <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" - label="Minimum mapping quality" - help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> + <expand macro="doNotExtendPairedEnds" /> + <expand macro="ignoreDuplicates" /> + <expand macro="minMappingQuality" /> <expand macro="missingDataAsZero" /> @@ -133,8 +127,46 @@ </change_format> </data> </outputs> + <tests> + <test> + <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> + <param name="outFileFormat" value="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <param name="type" value="no" /> + <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" /> + </test> + <test> + <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> + <param name="outFileFormat" value="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" /> + </test> + <test> + <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> + <param name="outFileFormat" value="bedgraph" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" /> + </test> + <test> + <param name="bamInput" value="phiX.bam" ftype="bam" /> + <param name="outFileFormat" value="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" /> + </test> + <test> + <param name="bamInput" value="phiX.bam" ftype="bam" /> + <param name="outFileFormat" value="bedgraph" /> + <param name="showAdvancedOpt" value="no" /> + <param name="binSize" value="10" /> + <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" /> + </test> + </tests> <help> - +<![CDATA[ **What it does** Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or @@ -160,7 +192,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/bamFingerprint.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/bamFingerprint.xml Mon Dec 22 18:56:27 2014 -0500 @@ -7,56 +7,54 @@ <import>deepTools_macros.xml</import> </macros> <command> +<![CDATA[ @multiple_input_bams@ - bamFingerprint + bamFingerprint - @THREADS@ + @THREADS@ - --bamfiles #echo " ".join($files) - --labels #echo " ".join($labels) + --bamfiles #echo " ".join($files) + --labels #echo " ".join($labels) - --fragmentLength $fragmentLength + --fragmentLength $fragmentLength - #set newoutFileName=str($outFileName)+".png" - --plotFile $newoutFileName + #set newoutFileName=str($outFileName)+".png" + --plotFile $newoutFileName - #if $output.showOutputSettings == "yes" - --plotFileFormat $output.outFileFormat - #if $output.saveRawCounts: - --outRawCounts '$outFileRawCounts' - #end if - #else - --plotFileFormat 'png' - #end if + #if $output.showOutputSettings == "yes" + --plotFileFormat $output.outFileFormat + #if $output.saveRawCounts: + --outRawCounts '$outFileRawCounts' + #end if + #else + --plotFileFormat 'png' + #end if - #if str($region).strip() != '': - --region '$region' - #end if + #if str($region).strip() != '': + --region '$region' + #end if - #if $advancedOpt.showAdvancedOpt == "yes": - --binSize '$advancedOpt.binSize' - --numberOfSamples '$advancedOpt.numberOfSamples' + #if $advancedOpt.showAdvancedOpt == "yes": + --binSize '$advancedOpt.binSize' + --numberOfSamples '$advancedOpt.numberOfSamples' + + $advancedOpt.doNotExtendPairedEnds + $advancedOpt.ignoreDuplicates + $advancedOpt.skipZeros - $advancedOpt.doNotExtendPairedEnds - $advancedOpt.ignoreDuplicates - $advancedOpt.skipZeros - - #if $advancedOpt.minMappingQuality: - --minMappingQuality '$advancedOpt.minMappingQuality' - #end if - #end if - ; mv $newoutFileName $outFileName - ; rm $temp_dir -rf + #if $advancedOpt.minMappingQuality: + --minMappingQuality '$advancedOpt.minMappingQuality' + #end if + #end if + ; mv $newoutFileName $outFileName + ; rm $temp_dir -rf +]]> </command> <inputs> <expand macro="multiple_input_bams" /> - - - <param name="fragmentLength" type="integer" value="200" min="1" - label="Length of the average fragment size"/> - + <expand macro="fragmentLength" /> <expand macro="region_limit_operation" /> <conditional name="advancedOpt"> @@ -66,29 +64,18 @@ </param> <when value="no" /> <when value="yes"> - <param name="binSize" type="integer" value="10000" min="1" + <param name="binSize" type="integer" value="500" min="1" label="Bin size in bp" help="Length in base pairs for a window used to sample the genome."/> - <param name="numberOfSamples" type="integer" value="100000" min="1" label="Number of samples" - help="Number of samples taken from the genome to compute the scaling factors"/> - - <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" - label="Do not extend paired ends" - help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> - - <param name="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." /> - - <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" - label="Minimum mapping quality" - help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> - - <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" - label ="Include zeros" - help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." /> + help="Number of samples taken from the genome to compute the scaling factors. (--numberOfSamples)"/> + + <expand macro="doNotExtendPairedEnds" /> + <expand macro="ignoreDuplicates" /> + <expand macro="minMappingQuality" /> + <expand macro="skipZeros" /> + </when> </conditional> @@ -116,8 +103,22 @@ </filter> </data> </outputs> + <tests> + <test> + <repeat name="input_files"> + <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> + </repeat> + <repeat name="input_files"> + <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" /> + </repeat> + <param name="fragmentLength" value="200" /> + <param name="showAdvancedOpt" value="no" /> + <param name="showOutputSettings" value="no" /> + <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" /> + </test> + </tests> <help> - +<![CDATA[ **What it does** This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal) @@ -146,7 +147,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/bamPEFragmentSize.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/bamPEFragmentSize.xml Mon Dec 22 18:56:27 2014 -0500 @@ -9,19 +9,17 @@ <command> <![CDATA[ bamPEFragmentSize - - @THREADS@ - - --bam '$bamInput' - --bamIndex ${bamInput.metadata.bam_index} - #if $histogram: - --histogram $histogram_outfile - #end if - > $outfile - + @THREADS@ + -bai ${bamInput.metadata.bam_index} + #if $histogram: + --histogram ./hist.png + #end if + '$bamInput' + > $outfile + && + mv ./hist.png $histogram_outfile ]]> </command> - <inputs> <param name="bamInput" format="bam" type="data" label="BAM file" help="The BAM file must be sorted."/> @@ -30,13 +28,21 @@ help="(--histogram)"/> </inputs> <outputs> - <data format="txt" name="outfile" label="${tool.name} on ${on_string}" /> - <data name="histogram_outfile" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)"> - <filter>histogram == '--histogram'</filter> + <data name="outfile" format="txt"/> + <data name="histogram_outfile" format="png"> + <filter>histogram is True</filter> </data> </outputs> + <tests> + <test> + <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" /> + <param name="histogram" value="True" /> + <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" /> + <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" /> + </test> + </tests> <help> - +<![CDATA[ **What it does** Given a BAM file it samples several regions to estimate the paird-end fragment length. @@ -44,7 +50,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/bigwigCompare.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/bigwigCompare.xml Mon Dec 22 18:56:27 2014 -0500 @@ -7,6 +7,7 @@ <import>deepTools_macros.xml</import> </macros> <command> +<![CDATA[ bigwigCompare @THREADS@ @@ -17,9 +18,9 @@ --outFileName '$outFileName' --outFileFormat '$outFileFormat' - --ratio $comparison.type + --ratio $comparison.comparison_select - #if $comparison.type in ['ratio','log2']: + #if $comparison.comparison_select in ['ratio','log2']: --pseudocount $comparison.pseudocount #end if @@ -34,15 +35,15 @@ --binSize $advancedOpt.binSize #end if +]]> </command> <inputs> <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" /> <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" /> - <conditional name="comparison"> - <param name="type" type="select" - label="How to compare the two files"> + <param name="comparison_select" type="select" + label="How to compare the two files" help="(--ratio)"> <option value="log2" selected="true">compute log2 of the number of reads ratio</option> <option value="ratio">compute the ratio of the number of reads</option> <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option> @@ -75,29 +76,45 @@ <when value="no" /> <when value="yes"> <param name="binSize" type="integer" value="50" min="1" - label="Bin size in bp" - help="Size of the bins in bp for the output of the bigwig/bedgraph file "/> - + label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length" + 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." /> - - <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment"/> - <param name="scaleFactor2" type="float" value="1" label="Scale factor for input"/> + 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" /> </when> </conditional> </inputs> <outputs> <data format="bigwig" name="outFileName"> - <change_format> - <when input="outFileFormat" value="bigwig" format="bigwig" /> - <when input="outFileFormat" value="bedgraph" format="bedgraph" /> - </change_format> + <change_format> + <when input="outFileFormat" value="bigwig" format="bigwig" /> + <when input="outFileFormat" value="bedgraph" format="bedgraph" /> + </change_format> </data> </outputs> - - <help> - + <tests> + <test> + <param name="bigwigFile1" value="1.bigwig" ftype="bigwig" /> + <param name="bigwigFile2" value="1.bigwig" ftype="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="outFileFormat" value="bigwig" /> + <param name="binSize" value="5" /> + <param name="comparison_select" value="ratio" /> + <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" /> + </test> + <test> + <param name="bigwigFile1" value="1.bigwig" ftype="bigwig" /> + <param name="bigwigFile2" value="1.bigwig" ftype="bigwig" /> + <param name="showAdvancedOpt" value="no" /> + <param name="outFileFormat" value="bedgraph" /> + <param name="binSize" value="10" /> + <param name="comparison_select" value="ratio" /> + <output name="outFileName" file="bigwigCompare_result2.bg" ftype="bedgraph" /> + </test> + </tests> + <help> +<![CDATA[ **What it does** This tool compares two bigwig files based on the number of mapped reads. To @@ -110,7 +127,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/computeGCBias.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/computeGCBias.xml Mon Dec 22 18:56:27 2014 -0500 @@ -7,6 +7,7 @@ <import>deepTools_macros.xml</import> </macros> <command> +<![CDATA[ ln -s $bamInput local_bamInput.bam; ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai; @@ -47,6 +48,7 @@ --biasPlot $outImageName --plotFileFormat $image_format #end if +]]> </command> <inputs> <param name="bamInput" format="bam" type="data" label="BAM file" @@ -54,11 +56,7 @@ <expand macro="reference_genome_source" /> <expand macro="effectiveGenomeSize" /> - - <param name="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."/> - + <expand macro="fragmentLength" /> <expand macro="region_limit_operation" /> <conditional name="advancedOpt"> @@ -69,21 +67,21 @@ <when value="no" /> <when value="yes"> <param name="sampleSize" type="integer" value="50000000" min="1" - label="Number of sampling points to be considered" /> - + 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."/> - + 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." /> + 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="" /> + help="(--extraSampling)" /> </when> </conditional> - <param name="image_format" type="select" label="GC bias plot" help="If given, a diagnostic image summarizing the GC bias found on the sample will be created."> + <param name="image_format" type="select" + label="GC bias plot" + help="If given, a diagnostic image summarizing the GC bias found on the sample will be created. (--plotFileFormat)"> <option value="none">No image</option> <option value="png" selected="true">Image in png format</option> <option value="pdf">Image in pdf format</option> @@ -93,8 +91,8 @@ </param> </inputs> <outputs> - <data format="tabular" name="outFileName" /> - <data format="png" name="outImageName" label="${tool.name} GC-bias Plot"> + <data name="outFileName" format="tabular" /> + <data name="outImageName" format="png" label="${tool.name} GC-bias Plot"> <filter> (( image_format != 'none' @@ -108,8 +106,21 @@ </change_format> </data> </outputs> + <tests> + <test> + <param name="bamInput" value="phiX.bam" ftype="bam" /> + <param name="image_format" value="png" /> + <param name="showAdvancedOpt" value="yes" /> + <param name="regionSize" value="1" /> + <param name="fragmentLength" value="100" /> + <param name="ref_source" value="history" /> + <param name="input1" value="phiX.2bit" /> + <output name="outFileName" file="computeGCBias_result1.tabular" ftype="tabular" /> + <output name="outImageName" file="computeGCBias_result1.png" ftype="png" /> + </test> + </tests> <help> - +<![CDATA[ **What it does** This tool computes the GC bias using the method proposed by Benjamini and Speed (2012) Nucleic Acids Res. (see below for more explanations) @@ -150,7 +161,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/computeMatrix.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/computeMatrix.xml Mon Dec 22 18:56:27 2014 -0500 @@ -7,191 +7,237 @@ <import>deepTools_macros.xml</import> </macros> <command> +<![CDATA[ #import tempfile - #set $temp_input_handle = tempfile.NamedTemporaryFile() - #set $temp_input_path = $temp_input_handle.name - #silent $temp_input_handle.close() + #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" >> $temp_input_path; - #if str($rf.label.value).strip(): - echo "\#$rf.label.value" >> $temp_input_path; - #else: - echo "\#$rf.regionsFile.name" >> $temp_input_path; - #end if - #end for + #for $rf in $regionsFiles: + cat "$rf.regionsFile" >> $temp_input_path; + #if str($rf.label.value).strip(): + echo "\#$rf.label.value" >> $temp_input_path; + #else: + echo "\#$rf.regionsFile.name" >> $temp_input_path; + #end if + #end for - - computeMatrix + computeMatrix - $mode.mode_select - --regionsFileName '$temp_input_path' - --scoreFileName '$scoreFile' - --outFileName '$outFileName' + $mode.mode_select + --regionsFileName '$temp_input_path' + --scoreFileName '$scoreFile' + --outFileName '$outFileName' - @THREADS@ + @THREADS@ - #if $output.showOutputSettings == "yes" - #if $output.saveData: - --outFileNameData '$outFileNameData' - #end if - #if $output.saveMatrix: - --outFileNameMatrix '$outFileNameMatrix' - #end if + #if $output.showOutputSettings == "yes" + #if $output.saveData: + --outFileNameData '$outFileNameData' + #end if + #if $output.saveMatrix: + --outFileNameMatrix '$outFileNameMatrix' + #end if - #if $output.saveSortedRegions: - --outFileSortedRegions '$outFileSortedRegions' - #end if - #end if + #if $output.saveSortedRegions: + --outFileSortedRegions '$outFileSortedRegions' + #end if + #end if - #if $mode.mode_select == "reference-point": - --referencePoint $mode.referencePoint - $mode.nanAfterEnd - --beforeRegionStartLength $mode.beforeRegionStartLength - --afterRegionStartLength $mode.afterRegionStartLength - #else - --regionBodyLength $mode.regionBodyLength - --startLabel "$mode.startLabel" - --endLabel "$mode.endLabel" - #if $mode.regionStartLength.regionStartLength_select == "yes": - --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength - --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength - #end if - #end if + #if $mode.mode_select == "reference-point": + --referencePoint $mode.referencePoint + $mode.nanAfterEnd + --beforeRegionStartLength $mode.beforeRegionStartLength + --afterRegionStartLength $mode.afterRegionStartLength + #else + --regionBodyLength $mode.regionBodyLength + --startLabel "$mode.startLabel" + --endLabel "$mode.endLabel" + #if $mode.regionStartLength.regionStartLength_select == "yes": + --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength + --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength + #end if + #end if - #if $advancedOpt.showAdvancedOpt == "yes": - --sortRegions '$advancedOpt.sortRegions' - --sortUsing '$advancedOpt.sortUsing' - --averageTypeBins '$advancedOpt.averageTypeBins' - $advancedOpt.missingDataAsZero - $advancedOpt.skipZeros - --binSize $advancedOpt.binSize + #if $advancedOpt.showAdvancedOpt == "yes": + --sortRegions '$advancedOpt.sortRegions' + --sortUsing '$advancedOpt.sortUsing' + --averageTypeBins '$advancedOpt.averageTypeBins' + $advancedOpt.missingDataAsZero + $advancedOpt.skipZeros + --binSize $advancedOpt.binSize - #if $advancedOpt.minThreshold: - --minThreshold $advancedOpt.minThreshold - #end if - #if $advancedOpt.maxThreshold: - --maxThreshold $advancedOpt.maxThreshold - #end if - #if $advancedOpt.scale: - --scale $advancedOpt.scale - #end if + #if $advancedOpt.minThreshold: + --minThreshold $advancedOpt.minThreshold + #end if + #if $advancedOpt.maxThreshold: + --maxThreshold $advancedOpt.maxThreshold + #end if + #if $advancedOpt.scale: + --scale $advancedOpt.scale + #end if + + #end if + ; rm $temp_input_path +]]> + </command> + <inputs> - #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."/> + </repeat> - <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."/> - </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)"/> - <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."/> + <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."> + <option value="scale-regions" selected="true">scale-regions</option> + <option value="reference-point">reference-point</option> + </param> - <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."> - <option value="scale-regions" selected="true">scale-regions</option> - <option value="reference-point">reference-point</option> - </param> - - <when value="scale-regions" > - <param name="regionBodyLength" type="integer" value="500" label="Distance in bp to which all regions are going to be fitted"/> - <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"." /> - <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)."/> - <conditional name="regionStartLength"> - <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions"> - <option value="no" selected="true">no</option> - <option value="yes">yes</option> + <when value="scale-regions" > + <param name="regionBodyLength" type="integer" value="500" + 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)" /> + <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)"/> + <conditional name="regionStartLength"> + <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions"> + <option value="no" selected="true">no</option> + <option value="yes">yes</option> + </param> + <when value="no" /> + <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)"/> + <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)"/> + </when> + </conditional> + </when> + <when value="reference-point"> + <param name="referencePoint" type="select" label="The reference point for the plotting"> + <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> + <option value="TES">end of region (e.g. TES)</option> + <option value="center">center of region</option> </param> - <when value="no" /> - <when value="yes"> - <param name="beforeRegionStartLength" type="integer" value="1000" min="1" optional="true" 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."/> - <param name="afterRegionStartLength" type="integer" value="1000" min="1" optional="true" 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."/> - </when> - </conditional> - </when> - - <when value="reference-point"> - <param name="referencePoint" type="select" label="The reference point for the plotting"> - <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> - <option value="TES">end of region (e.g. TES)</option> - <option value="center">center of region</option> - </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."/> - <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."/> - <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."/> - </when> - </conditional> + <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)"/> + <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)"/> + <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)"/> + </when> + </conditional> - <expand macro="input_graphic_output_settings"> - <expand macro="input_save_matrix_values" /> - </expand> + <expand macro="input_graphic_output_settings"> + <expand macro="input_save_matrix_values" /> + </expand> - <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"> - <param name="binSize" type="integer" value="100" min="1" optional="true" label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length" /> - <param name="sortRegions" type="select" label="Sort regions" - help="Whether the output file should present the regions sorted."> - <option value="no" selected="true">no ordering</option> - <option value="descend">descending order</option> - <option value="ascend">ascending order</option> - </param> + <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"> + <param name="binSize" type="integer" value="10" min="1" + label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length" + help="(--binSize)"/> + <param name="sortRegions" type="select" label="Sort regions" + help="Whether the output file should present the regions sorted."> + <option value="no" selected="true">no ordering</option> + <option value="descend">descending order</option> + <option value="ascend">ascending order</option> + </param> - <param name="sortUsing" type="select" label="Method used for sorting." help="The value is computed for each row." > - <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> + <param name="sortUsing" type="select" label="Method used for sorting" + help="The value is computed for each row. (--sortUsing)" > + <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> - <param name="averageTypeBins" type="select" label="Define the type of statistic that should be displayed." help="The value is computed for each bin."> - <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="std">std</option> - </param> + <param name="averageTypeBins" type="select" + label="Define the type of statistic that should be displayed." + help="The value is computed for each bin. (--averageTypeBins)"> + <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="std">std</option> + </param> - <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)."/> - <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."/> - <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."/> - <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."/> - <param name="scale" type="float" optional="true" label="Scale" help="If set, all values are multiplied by this number."/> - </when> - </conditional> - + <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)"/> + <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)"/> + <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)"/> + <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)"/> + <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 ${on_string}: Matrix" /> - <expand macro="output_graphic_outputs" /> - <expand macro="output_save_matrix_values" /> - </outputs> + <outputs> + <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> + <expand macro="output_graphic_outputs" /> + <expand macro="output_save_matrix_values" /> + </outputs> <!-- computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 --> <tests> <test> - <param name="regionsFile" value="test2.bed" ftype="bed" /> - <param name="scoreFile" value="test.bw" ftype="bigwig" /> - <param name="advancedOpt.binSize" value="1" /> - <param name="mode.beforeRegionStartLength" value="100" /> - <param name="mode.afterRegionStartLength" value="100" /> - <output name="outFileName" file="master.mat.gz" ftype="bgzip" compare="sim_size" delta="100" /> + <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" /> + <param name="scoreFile" value="bamCoverage_result4.bw" ftype="bigwig" /> + <param name="showAdvancedOpt" value="yes" /> + <param name="mode_select" value="reference-point" /> + <param name="binSize" value="10" /> + <param name="sortUsing" value="sum" /> + <param name="averageTypeBins" value="sum" /> + <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" /> + </test> + <test> + <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> + <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" /> + <param name="showAdvancedOpt" value="yes" /> + <param name="mode_select" value="reference-point" /> + <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" /> </test> </tests> <help> - +<![CDATA[ **What it does** This tool prepares an intermediary file (a gzipped table of values) @@ -217,7 +263,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/correctGCBias.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/correctGCBias.xml Mon Dec 22 18:56:27 2014 -0500 @@ -7,86 +7,53 @@ <import>deepTools_macros.xml</import> </macros> <command> - #import tempfile - #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) - - #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) - #set $temp_bam_path = $temp_bam_handle.name + '.bam' - #silent $temp_bam_handle.close() - #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path)) - #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path)) - +<![CDATA[ + ln -s $bamInput local_bamInput.bam; + ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai; correctGCBias - - @THREADS@ - - --bamfile '$temp_bam_path' - --GCbiasFrequenciesFile $GCbiasFrequenciesFile + @THREADS@ + --bamfile local_bamInput.bam + --GCbiasFrequenciesFile $GCbiasFrequenciesFile - @reference_genome_source@ - - - #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": - --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize - #else: - --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt - #end if + @reference_genome_source@ - #if str($region).strip() != '': - --region '$region' - #end if + #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific": + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize + #else: + --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt + #end if - #if $advancedOpt.showAdvancedOpt == "yes": - --binSize '$advancedOpt.binSize' - #end if - - ###set newoutFileName="corrected."+str($outFileFormat) - ##--correctedFile $newoutFileName; - --correctedFile "corrected.bam"; - - ##mv $newoutFileName $outFileName - mv "corrected.bam" $outFileName + #if str($region).strip() != '': + --region '$region' + #end if + --correctedFile $outFileName +]]> </command> <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."/> + <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."/> <expand macro="reference_genome_source" /> <expand macro="effectiveGenomeSize" /> - - <!-- - <param name="outFileFormat" type="select" label="File format of the output"> - <option value="bam">bam</option> - <option value="bw">bigwig</option> - <option value="bg">bedgraph</option> - </param> - --> <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"> - <param name="binSize" type="integer" value="50" min="1" - label="Bin size in bp" - help="Size of the bins in bp for the output of the bigwig/bedgraph file."/> - </when> - </conditional> </inputs> <outputs> - <data format="bam" name="outFileName"> - <!--<change_format> - <when input="outFileFormat" value="bw" format="bigwig" /> - <when input="outFileFormat" value="bam" format="bam" /> - <when input="outFileFormat" value="bg" format="bedgraph" /> - </change_format>--> - </data> + <data format="bam" name="outFileName" /> </outputs> + <tests> + <test> + <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" /> + <param name="bamInput" value="phiX.bam" ftype="bam" /> + <param name="ref_source" value="history" /> + <param name="input1" value="phiX.2bit" /> + <param name="effectiveGenomeSize_opt" value="specific" /> + <param name="effectiveGenomeSize" value="5386" /> + <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" compare="sim_size" /> + </test> + </tests> <help> - +<![CDATA[ **What it does** This tool requires the output from computeGCBias to correct a given BAM file according to the method proposed by @@ -103,7 +70,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/deepTools_macros.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/deepTools_macros.xml Mon Dec 22 18:56:27 2014 -0500 @@ -10,28 +10,16 @@ </param> <when value="no" /> <when value="yes"> - <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" - label="Do not extend paired ends" - help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/> - - <param name="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." /> - - <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" - label="Minimum mapping quality" - help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/> - + <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." /> - + 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."/> - + 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."/> - + help="If not specified the value is set automatically. (--zMax)"/> <expand macro="colormap" /> </when> </conditional> @@ -40,9 +28,8 @@ <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"" /> + 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@">1.5.9.1</token> <xml name="requirements"> @@ -87,9 +74,9 @@ </when> <when value="yes" /> </conditional> + </xml> - </xml> - <token name="@kmeans_clusterin@"> + <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: @@ -99,6 +86,41 @@ #end if </token> + <xml name="doNotExtendPairedEnds"> + <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue="" + label="Do not extend paired ends" + help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available. (--doNotExtendPairedEnds)"/> + </xml> + + <xml name="ignoreDuplicates"> + <param name="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. (--ignoreDuplicates)" /> + </xml> + + <xml name="minMappingQuality"> + <param name="minMappingQuality" type="integer" optional="true" value="1" min="1" + label="Minimum mapping quality" + help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere. (--minMappingQuality)"/> + </xml> + + <xml name="skipZeros"> + <param name="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 might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined. (--skipZeros)" /> + </xml> + + <xml name="fragmentLength"> + <param name="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. (--fragmentLength)"/> + </xml> + + <xml name="scaleFactor"> + <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:" /> @@ -109,9 +131,11 @@ <regex match="Traceback" /> </stdio> </xml> + <xml name="pseudocount"> <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> </xml> + <token name="@REFERENCES@"> .. class:: infomark
--- a/heatmapper.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/heatmapper.xml Mon Dec 22 18:56:27 2014 -0500 @@ -7,6 +7,7 @@ <import>deepTools_macros.xml</import> </macros> <command> +<![CDATA[ heatmapper --matrixFile $matrixFile @@ -81,9 +82,10 @@ $advancedOpt.onePlotPerGroup - @kmeans_clusterin@ + @KMEANS_CLUSTERING@ #end if +]]> </command> <inputs> <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/> @@ -125,22 +127,31 @@ <option value="std">std</option> </param> - <param name="missingDataColor" type="text" label="Missing data color" value="black" optional="true" help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. Alternatively colors can be specified using the #rrggbb notation." /> + <param name="missingDataColor" type="text" value="black" optional="true" label="Missing data color" + help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. Alternatively colors can be specified using the #rrggbb notation." /> <expand macro="colormap" /> - <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/> - <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/> - <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/> - <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/> + <param name="zMin" type="float" value="" size="3" + label="Minimum value for the heatmap intensities. Leave empty for automatic values"/> + <param name="zMax" type="float" value="" size="3" + label="Maximum value for the heatmap intensities. Leave empty for automatic values"/> + <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" + label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/> + <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" + label="Description for the x-axis label" /> + <param name="yAxisLabel" type="text" value="genes" size="30" + label="Description for the y-axis label for the top panel" /> - <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" label="Description for the x-axis label" /> - <param name="yAxisLabel" type="text" value="genes" size="30" label="Description for the y-axis label for the top panel" /> + <param name="heatmapWidth" type="float" value="7.5" min="1" max="100" + label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/> + <param name="heatmapHeight" type="float" value="25" min="3" max="100" + label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/> - <param name="heatmapWidth" type="float" value="7.5" min="1" max="100" label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/> - <param name="heatmapHeight" type="float" value="25" min="3" max="100" label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/> - - <param name="whatToShow" type="select" label="What to show" help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar."> + <param name="whatToShow" type="select" label="What to show" + help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar."> <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option> <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option> <option value="heatmap only">heatmap only</option> @@ -148,10 +159,16 @@ <option value="colorbar only">colorbar only</option> </param> - <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"." /> - <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)."/> + <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"." /> + <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)."/> - <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." /> + <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." /> <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."> @@ -160,13 +177,13 @@ </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." /> + <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="kmeans_clustering" /> - </when> </conditional> </inputs> @@ -177,12 +194,12 @@ </outputs> <tests> <test> - <param name="matrixFile" value="master.mat.gz" ftype="bgzip" /> - <output name="outFileName" file="master.png" ftype="png" compare="sim_size" delta="100" /> + <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" /> + <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" /> </test> </tests> <help> - +<![CDATA[ **What it does** The heatmapper visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes. @@ -205,7 +222,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- a/profiler.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/profiler.xml Mon Dec 22 18:56:27 2014 -0500 @@ -9,6 +9,7 @@ <import>deepTools_macros.xml</import> </macros> <command> +<![CDATA[ profiler --matrixFile $matrixFile @@ -65,9 +66,10 @@ --yAxisLabel '$advancedOpt.yAxisLabel' #end if - @kmeans_clusterin@ + @KMEANS_CLUSTERING@ #end if +]]> </command> <inputs> <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/> @@ -78,8 +80,12 @@ </param> <when value="no" /> <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"." /> - <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)."/> + <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"." /> + <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)."/> </when> </conditional> @@ -115,17 +121,30 @@ <option value="se">add standard error</option> <option value="overlapped_lines">overlapped lines</option> </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." /> - <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)"> - <validator type="expression" message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator> + <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." /> + <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)"> + <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."/> - <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/> - <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/> - <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" /> - <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" /> + <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."/> + <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" + label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" /> + <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" + label="Description for the x-axis label" /> + <param name="yAxisLabel" type="text" value="" size="50" + label="Description for the y-axis label for the top panel" /> <expand macro="kmeans_clustering" /> @@ -137,7 +156,7 @@ <expand macro="output_graphic_outputs" /> </outputs> <help> - +<![CDATA[ **What it does** This tool plots the average enrichments over all genomic @@ -158,7 +177,7 @@ ----- @REFERENCES@ - +]]> </help> <expand macro="citations" /> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamCompare_result1.bg Mon Dec 22 18:56:27 2014 -0500 @@ -0,0 +1,1 @@ +chrM 0 16569 1.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamCoverage_result3.bg Mon Dec 22 18:56:27 2014 -0500 @@ -0,0 +1,12 @@ +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
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamPEFragmentSize_result1.txt Mon Dec 22 18:56:27 2014 -0500 @@ -0,0 +1,9 @@ +Sample size: 3 + +Min.: 241.0 +1st Qu.: 241.5 +Mean: 244.666666667 +Median: 242.0 +3rd Qu.: 246.5 +Max.: 251.0 +Std: 4.49691252108
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bigwigCompare_result2.bg Mon Dec 22 18:56:27 2014 -0500 @@ -0,0 +1,5 @@ +chr21 0 10000000 1.0 +chr21 10000000 20000000 1.0 +chr21 20000000 30000000 1.0 +chr21 30000000 40000000 1.0 +chr21 40000000 48129895 1.0
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/computeMatrix1.bed Mon Dec 22 18:56:27 2014 -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 22 18:56:27 2014 -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/phiX.fasta Mon Dec 22 18:56:27 2014 -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 +
--- a/test-data/test2.bed Thu Sep 18 16:58:56 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -ch1 100 150 CG11023 0 + -ch2 150 175 cda5 0 - -ch3 100 125 cda8 0 + -#Group 1 -ch1 75 125 C11023 0 + -ch2 125 150 ca5 0 - -ch3 75 100 ca8 0 + -#Group 2
--- a/tool_dependencies.xml Thu Sep 18 16:58:56 2014 -0400 +++ b/tool_dependencies.xml Mon Dec 22 18:56:27 2014 -0500 @@ -3,14 +3,14 @@ <package name="samtools" version="0.1.19"> <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="numpy" version="1.7.1"> - <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="numpy" version="1.9"> + <repository changeset_revision="49a8bba001d7" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="matplotlib" version="1.2.1"> - <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="matplotlib" version="1.4"> + <repository changeset_revision="1bf5edeeaf42" name="package_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <package name="scipy" version="0.12.0"> - <repository changeset_revision="a983dc7c8103" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <package name="scipy" version="0.14"> + <repository changeset_revision="8512070824f3" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="pysam" version="0.7.7"> <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> @@ -69,14 +69,14 @@ <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="bx-python" version="12-2013" /> </repository> - <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="numpy" version="1.7.1" /> + <repository changeset_revision="49a8bba001d7" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="numpy" version="1.9" /> </repository> - <repository changeset_revision="de9c362fb3f2" name="package_matplotlib_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="matplotlib" version="1.2.1" /> + <repository changeset_revision="1bf5edeeaf42" name="package_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="matplotlib" version="1.4" /> </repository> - <repository changeset_revision="a983dc7c8103" name="package_scipy_0_12" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="scipy" version="0.12.0" /> + <repository changeset_revision="8512070824f3" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="scipy" version="0.14" /> </repository> </action> <action type="setup_python_environment">