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comparison computeMatrix.xml @ 1:21d563d5f2b2 draft

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author bgruening
date Mon, 05 Aug 2013 10:09:51 -0400
parents 09b65c12a75a
children c8a0dc481493
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0:09b65c12a75a 1:21d563d5f2b2
1 <tool id="computeMatrix" name="computeMatrix" version="1.0"> 1 <tool id="computeMatrix" name="computeMatrix" version="1.0">
2 <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description> 2 <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement> 4 <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 computeMatrix 7 computeMatrix
8
9 ##ToDo
10 --numberOfProcessors 4
11
8 $mode.mode_select 12 $mode.mode_select
9 --regionsFileName '$regionsFile' 13 --regionsFileName '$regionsFile'
10 --scoreFileName '$scoreFile' 14 --scoreFileName '$scoreFile'
11 --outFileName '$outFileName' 15 --outFileName '$outFileName'
12 16
13 #if $output.showOutputSettings == "yes" 17 #if $output.showOutputSettings == "yes"
14 #if $output.saveData: 18 #if $output.saveData:
15 --outFileNameData '$outFileNameData' 19 --outFileNameData '$outFileNameData'
16 #end if 20 #end if
17 #if $output.saveMatrix: 21 #if $output.saveMatrix:
18 --outFileNameMatrix '$outFileNameMatrix' 22 --outFileNameMatrix '$outFileNameMatrix'
19 #end if 23 #end if
20 24
21 #if $output.saveSortedRegions: 25 #if $output.saveSortedRegions:
22 --outFileSortedRegions '$outFileSortedRegions' 26 --outFileSortedRegions '$outFileSortedRegions'
23 #end if 27 #end if
24 #end if 28 #end if
25 29
26 #if $mode.mode_select == "reference-point": 30 #if $mode.mode_select == "reference-point":
27 --referencePoint $mode.referencePoint 31 --referencePoint $mode.referencePoint
28 $mode.nanAfterEnd 32 $mode.nanAfterEnd
29 --beforeRegionStartLength $mode.beforeRegionStartLength 33 --beforeRegionStartLength $mode.beforeRegionStartLength
30 --afterRegionStartLength $mode.afterRegionStartLength 34 --afterRegionStartLength $mode.afterRegionStartLength
35 #if $mode.regionStartLength.regionStartLength_select == "yes": 39 #if $mode.regionStartLength.regionStartLength_select == "yes":
36 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength 40 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
37 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength 41 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
38 #end if 42 #end if
39 #end if 43 #end if
40 44
41 #if $advancedOpt.showAdvancedOpt == "yes": 45 #if $advancedOpt.showAdvancedOpt == "yes":
42 --sortRegions '$advancedOpt.sortRegions' 46 --sortRegions '$advancedOpt.sortRegions'
43 --sortUsing '$advancedOpt.sortUsing' 47 --sortUsing '$advancedOpt.sortUsing'
44 --averageTypeBins '$advancedOpt.averageTypeBins' 48 --averageTypeBins '$advancedOpt.averageTypeBins'
45 $advancedOpt.missingDataAsZero 49 $advancedOpt.missingDataAsZero
46 $advancedOpt.skipZeros 50 $advancedOpt.skipZeros
47 -bs $advancedOpt.binSize 51 --binSize $advancedOpt.binSize
48 52
49 #if $advancedOpt.minThreshold: 53 #if $advancedOpt.minThreshold:
50 --minThreshold $advancedOpt.minThreshold 54 --minThreshold $advancedOpt.minThreshold
51 #end if 55 #end if
52 #if $advancedOpt.maxThreshold: 56 #if $advancedOpt.maxThreshold:
53 --maxThreshold $advancedOpt.maxThreshold 57 --maxThreshold $advancedOpt.maxThreshold
54 #end if 58 #end if
55 #if $advancedOpt.scale: 59 #if $advancedOpt.scale:
56 --scale $advancedOpt.scale 60 --scale $advancedOpt.scale
57 #end if 61 #end if
58 62
59 #end if 63 #end if
60 --numberOfProcessors 4 64
61 </command> 65 </command>
62 <inputs> 66 <inputs>
63 <param name="regionsFile" format="bed,gff" type="data" label="Regions to plot" help="File, in BED or GFF format, containing the regions to plot."/> 67 <param name="regionsFile" format="bed,gff" type="data" label="Regions to plot" help="File, in BED or GFF format, containing the regions to plot."/>
64 <param name="scoreFile" format="bigwig,bam" type="data" label="Score file" help="Either a bigWig file (containing a score, usually covering the whole genome) or a BAM file. For this last case, coverage counts will be used for the heatmap."/> 68 <param name="scoreFile" format="bigwig,bam" type="data" label="Score file" help="Either a bigWig file (containing a score, usually covering the whole genome) or a BAM file. For this last case, coverage counts will be used for the heatmap."/>
65 69
66 <conditional name="mode" > 70 <conditional name="mode" >
67 <param name="mode_select" type="select" label="computeMatrix has two main output options" help="In the scale-regions mode, all regions in the BED/GFF 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/GFF 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."> 71 <param name="mode_select" type="select" label="computeMatrix has two main output options" help="In the scale-regions mode, all regions in the BED/GFF 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/GFF 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.">
68 <option value="scale-regions" selected="true">scale-regions</option> 72 <option value="scale-regions" selected="true">scale-regions</option>
69 <option value="reference-point">reference-point</option> 73 <option value="reference-point">reference-point</option>
70 </param> 74 </param>
71 75
72 <when value="scale-regions" > 76 <when value="scale-regions" >
73 <param name="regionBodyLength" type="integer" value="500" label="Distance in bp to which all regions are going to be fitted"/> 77 <param name="regionBodyLength" type="integer" value="500" label="Distance in bp to which all regions are going to be fitted"/>
74 <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. &quot;peak start&quot;." /> 78 <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. &quot;peak start&quot;." />
75 <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)."/> 79 <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)."/>
76 <conditional name="regionStartLength"> 80 <conditional name="regionStartLength">
110 <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/> 114 <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/>
111 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/> 115 <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/>
112 <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/> 116 <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
113 </when> 117 </when>
114 </conditional> 118 </conditional>
115 119
116
117 <conditional name="advancedOpt" > 120 <conditional name="advancedOpt" >
118 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 121 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
119 <option value="no" selected="true">no</option> 122 <option value="no" selected="true">no</option>
120 <option value="yes">yes</option> 123 <option value="yes">yes</option>
121 </param> 124 </param>
122 <when value="no" /> 125 <when value="no" />
123 <when value="yes"> 126 <when value="yes">
124
125 <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" /> 127 <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" />
126
127 <param name="sortRegions" type="select" label="Sort regions" 128 <param name="sortRegions" type="select" label="Sort regions"
128 help="Whether the output file should present the regions sorted."> 129 help="Whether the output file should present the regions sorted.">
129 <option value="no" selected="true">no ordering</option> 130 <option value="no" selected="true">no ordering</option>
130 <option value="descend">descending order</option> 131 <option value="descend">descending order</option>
131 <option value="ascend">ascending order</option> 132 <option value="ascend">ascending order</option>
132 </param> 133 </param>
133 134
134 <param name="sortUsing" type="select" label="Method used for sorting." help="The value is computed for each row." > 135 <param name="sortUsing" type="select" label="Method used for sorting." help="The value is computed for each row." >
135 <option value="mean" selected="true">mean</option> 136 <option value="mean" selected="true">mean</option>
136 <option value="median">median</option> 137 <option value="median">median</option>
137 <option value="min">min</option> 138 <option value="min">min</option>
138 <option value="max">max</option> 139 <option value="max">max</option>
139 <option value="sum">sum</option> 140 <option value="sum">sum</option>
140 <option value="region_length">region length</option> 141 <option value="region_length">region length</option>
141 </param> 142 </param>
142 143
143 <param name="averageTypeBins" type="select" label="Define the type of statistic that should be used over the bin size range"> 144 <param name="averageTypeBins" type="select" label="Define the type of statistic that should be used over the bin size range">
144 <option value="mean" selected="true">mean</option> 145 <option value="mean" selected="true">mean</option>
145 <option value="median">median</option> 146 <option value="median">median</option>
146 <option value="min">min</option> 147 <option value="min">min</option>
147 <option value="max">max</option> 148 <option value="max">max</option>
148 <option value="sum">sum</option> 149 <option value="sum">sum</option>
149 <option value="std">std</option> 150 <option value="std">std</option>
150 </param> 151 </param>
151 152
152 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" label="Indicate missing data as zero" help="Only for bigwig input! Set to &quot;yes&quot;, 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 &quot;Missing data color&quot; options of the heatmapper for additional options)."/> 153 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" label="Indicate missing data as zero" help="Only for bigwig input! Set to &quot;yes&quot;, 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 &quot;Missing data color&quot; options of the heatmapper for additional options)."/>
153
154 <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."/> 154 <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."/>
155
156 <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."/> 155 <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."/>
157 <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."/> 156 <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."/>
158 <param name="scale" type="float" optional="true" label="Scale" help="If set, all values are multiplied by this number."/> 157 <param name="scale" type="float" optional="true" label="Scale" help="If set, all values are multiplied by this number."/>
159 </when> 158 </when>
160 </conditional> 159 </conditional>
202 201
203 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ 202 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
204 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de 203 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
205 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de 204 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
206 </help> 205 </help>
207
208 </tool> 206 </tool>