Mercurial > repos > bgruening > deeptools_compute_matrix
diff computeMatrix.xml @ 0:14cb57237e46 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
| author | bgruening |
|---|---|
| date | Mon, 25 Jan 2016 20:26:32 -0500 |
| parents | |
| children | 275ed3e83de0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/computeMatrix.xml Mon Jan 25 20:26:32 2016 -0500 @@ -0,0 +1,264 @@ +<tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0"> + <description>prepares data for plotting a heatmap or a profile of given regions</description> + <macros> + <token name="@BINARY@">computeMatrix</token> + <import>deepTools_macros.xml</import> + </macros> + <expand macro="requirements" /> + <command> +<![CDATA[ + #import tempfile + + @BINARY@ + + $mode.mode_select + --regionsFileName + #for $rf in $regionsFiles: + '$rf.regionsFile' + #end for + --scoreFileName + #for $bw in $scoreFileName: + '$bw' + #end for + --outFileName '$outFileName' + + @THREADS@ + + #if $output.showOutputSettings == "yes" + #if $output.saveMatrix: + --outFileNameMatrix '$outFileNameMatrix' + #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 + #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.skipNAs + $advancedOpt.skipZeros + --binSize $advancedOpt.binSize + + #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '': + --minThreshold $advancedOpt.minThreshold + #end if + #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '': + --maxThreshold $advancedOpt.maxThreshold + #end if + #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': + --scale $advancedOpt.scale + #end if + + #end if +]]> + </command> + <inputs> + + <repeat name="regionsFiles" title="Select regions" min="1"> + <param name="regionsFile" format="bed" type="data" label="Regions to plot" + help="File, in BED format, containing the regions to plot."/> + </repeat> + + <param name="scoreFileName" format="bigwig" type="data" + label="Score file" multiple="True" + help="You can generate a bigWig file from either a + bedGraph or WIG file using UCSC tools or from a BAM file using the + bamCoverage tool. (--scoreFileName)"/> + + <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 (in bases) 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 (upstream) and/or after (downstream) + the reference point will be considered."> + <option value="scale-regions" selected="true">scale-regions</option> + <option value="reference-point">reference-point</option> + </param> + + <when value="scale-regions" > + <param argument="--regionBodyLength" type="integer" value="500" + label="Distance in bases to which all regions are going to be fit" help=""/> + <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 argument="--beforeRegionStartLength" type="integer" value="1000" min="1" + label="Distance upstream of the region start position" + help="If the regions are genes, this would be the + distance upstream of the transcription start site."/> + <param argument="--afterRegionStartLength" type="integer" value="1000" min="1" + label="Distance downstream of the region end position" + 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. (--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> + + <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="Length, in bases, of non-overlapping bins used for averaging the score over the regions length" + help="(--binSize)"/> + + <expand macro="sortRegions" /> + <expand macro="sortUsing" /> + + <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="" checked="False" + label="Convert missing values to 0?." + help="If set to 'yes', missing values (NAs) are converted to 0. + The default is to ignore such cases, which will be + depicted as black areas once a heatmap is created." /> + + <expand macro="skipZeros" /> + <expand macro="skipNAs" /> + + <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="deeptools_compute_matrix_archive" 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="computeMatrix1.bed" ftype="bed" /> + <param name="scoreFileName" 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="skipNAs" value="False" /> + <param name="beforeRegionStartLength" value="10" /> + <param name="afterRegionStartLength" value="10" /> + <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> + </test> + <test> + <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> + <param name="scoreFileName" 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="deeptools_compute_matrix_archive" compare="sim_size" /> + </test> + <test> + <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> + <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" /> + <param name="showAdvancedOpt" value="yes" /> + <param name="mode_select" value="scale-regions" /> + <param name="endLabel" value="END" /> + <param name="regionStartLength" value="yes" /> + <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> + </test> + </tests> + <help> +<![CDATA[ +**What it does** + +This tool prepares an intermediate file (a gzipped table of values) +that contains scores associated with genomic regions and can be used +afterwards to plot a heatmap or profile. + +Genomic regions can really be anything - genes, parts of genes, ChIP-seq +peaks, favorite genome regions... as long as you provide a proper file +in BED or INTERVAL format. If you would like to compare different groups of regions +(i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group. + +computeMatrix can also be used to filter and sort +regions according to their score by making use of its advanced output options. + + +.. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png + :alt: Relationship between computeMatrix, heatmapper and profiler + + +You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/master/content/tools/computeMatrix.html + + +----- + +@REFERENCES@ +]]> + </help> + <expand macro="citations" /> +</tool>