Mercurial > repos > bgruening > deeptools
annotate computeMatrix.xml @ 68:1a0565ddac27 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
| author | galaxyp |
|---|---|
| date | Sat, 30 May 2015 17:59:12 -0400 |
| parents | 1dbd76a58d8b |
| children |
| rev | line source |
|---|---|
| 61 | 1 <tool id="deeptools_computeMatrix" name="computeMatrix" version="@WRAPPER_VERSION@.0"> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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2 <description>preparation step to plot a heatmap or a profile</description> |
| 61 | 3 <macros> |
| 4 <token name="@BINARY@">computeMatrix</token> | |
| 5 <import>deepTools_macros.xml</import> | |
| 6 </macros> | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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7 <expand macro="requirements" /> |
| 61 | 8 <command> |
| 9 <![CDATA[ | |
| 10 #import tempfile | |
| 11 | |
| 12 #for $rf in $regionsFiles: | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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13 cat "$rf.regionsFile" >> ./temp_input_path; |
| 61 | 14 #if str($rf.label.value).strip(): |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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15 echo "\#$rf.label.value" >> ./temp_input_path; |
| 61 | 16 #else: |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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17 echo "\#$rf.regionsFile.name" >> ./temp_input_path; |
| 61 | 18 #end if |
| 19 #end for | |
| 20 | |
| 21 computeMatrix | |
| 22 | |
| 23 $mode.mode_select | |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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24 --regionsFileName ./temp_input_path |
| 61 | 25 --scoreFileName '$scoreFile' |
| 26 --outFileName '$outFileName' | |
| 27 | |
| 28 @THREADS@ | |
| 29 | |
| 30 #if $output.showOutputSettings == "yes" | |
| 31 #if $output.saveData: | |
| 32 --outFileNameData '$outFileNameData' | |
| 33 #end if | |
| 34 #if $output.saveMatrix: | |
| 35 --outFileNameMatrix '$outFileNameMatrix' | |
| 36 #end if | |
| 37 | |
| 38 #if $output.saveSortedRegions: | |
| 39 --outFileSortedRegions '$outFileSortedRegions' | |
| 40 #end if | |
| 41 #end if | |
| 42 | |
| 43 #if $mode.mode_select == "reference-point": | |
| 44 --referencePoint $mode.referencePoint | |
| 45 $mode.nanAfterEnd | |
| 46 --beforeRegionStartLength $mode.beforeRegionStartLength | |
| 47 --afterRegionStartLength $mode.afterRegionStartLength | |
| 48 #else | |
| 49 --regionBodyLength $mode.regionBodyLength | |
| 50 --startLabel "$mode.startLabel" | |
| 51 --endLabel "$mode.endLabel" | |
| 52 #if $mode.regionStartLength.regionStartLength_select == "yes": | |
| 53 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength | |
| 54 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength | |
| 55 #end if | |
| 56 #end if | |
| 57 | |
| 58 #if $advancedOpt.showAdvancedOpt == "yes": | |
| 59 --sortRegions '$advancedOpt.sortRegions' | |
| 60 --sortUsing '$advancedOpt.sortUsing' | |
| 61 --averageTypeBins '$advancedOpt.averageTypeBins' | |
| 62 $advancedOpt.missingDataAsZero | |
| 63 $advancedOpt.skipZeros | |
| 64 --binSize $advancedOpt.binSize | |
| 65 | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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66 #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '': |
| 61 | 67 --minThreshold $advancedOpt.minThreshold |
| 68 #end if | |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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69 #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '': |
| 61 | 70 --maxThreshold $advancedOpt.maxThreshold |
| 71 #end if | |
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1dbd76a58d8b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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72 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': |
| 61 | 73 --scale $advancedOpt.scale |
| 74 #end if | |
| 75 | |
| 76 #end if | |
| 77 ]]> | |
| 78 </command> | |
| 79 <inputs> | |
| 80 | |
| 81 <repeat name="regionsFiles" title="regions to plot" min="1"> | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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82 <param name="regionsFile" format="bed" type="data" label="Regions to plot" |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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83 help="File, in BED format, containing the regions to plot."/> |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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84 <param name="label" type="text" size="30" optional="true" value="" label="Label" |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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85 help="Label to use in the output."/> |
| 61 | 86 </repeat> |
| 87 | |
| 88 <param name="scoreFile" format="bigwig" type="data" | |
| 89 label="Score file" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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90 help="Should be a bigWig file (containing a score, usually covering |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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91 the whole genome). You can generate a bigWig file either from a |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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92 bedGraph or WIG file using UCSC tools or from a BAM file using the |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
iuc
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93 deepTool bamCoverage. (-scoreFile)"/> |
| 61 | 94 |
| 95 <conditional name="mode" > | |
| 96 <param name="mode_select" type="select" | |
| 97 label="computeMatrix has two main output options" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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98 help="In the scale-regions mode, all regions in the BED file are |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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99 stretched or shrunk to the same length (bp) that is indicated |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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100 by the user. Reference-point refers to a position within the BED |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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101 regions (e.g start of region). In the reference-point mode only |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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102 those genomic positions before (downstream) and/or after (upstream) |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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103 the reference point will be plotted."> |
| 61 | 104 <option value="scale-regions" selected="true">scale-regions</option> |
| 105 <option value="reference-point">reference-point</option> | |
| 106 </param> | |
| 107 | |
| 108 <when value="scale-regions" > | |
| 109 <param name="regionBodyLength" type="integer" value="500" | |
| 110 label="Distance in bp to which all regions are going to be fitted" help="(--regionBodyLength)"/> | |
| 111 <param name="startLabel" type="text" value="TSS" size="10" | |
| 112 label="Label for the region start" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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113 help ="Label shown in the plot for the start of the region. |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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114 Default is TSS (transcription start site), but could be changed to anything, |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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115 e.g. "peak start". (--startLabel)" /> |
| 61 | 116 <param name="endLabel" type="text" value="TES" size="10" |
| 117 label="Label for the region end" | |
| 118 help="Label shown in the plot for the region end. Default is TES (transcription end site). (--endLabel)"/> | |
| 119 <conditional name="regionStartLength"> | |
| 120 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions"> | |
| 121 <option value="no" selected="true">no</option> | |
| 122 <option value="yes">yes</option> | |
| 123 </param> | |
| 124 <when value="no" /> | |
| 125 <when value="yes"> | |
| 126 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" | |
| 127 label="Distance upstream of the start site of the regions defined in the region file" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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128 help="If the regions are genes, this would be the |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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129 distance upstream of the transcription start site. (--beforeRegionStartLength)"/> |
| 61 | 130 <param name="afterRegionStartLength" type="integer" value="1000" min="1" |
| 131 label="Distance downstream of the end site of the given regions" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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132 help="If the regions are genes, this would be the |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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133 distance downstream of the transcription end site. (--afterRegionStartLength)"/> |
| 61 | 134 </when> |
| 135 </conditional> | |
| 136 </when> | |
| 137 <when value="reference-point"> | |
| 138 <param name="referencePoint" type="select" label="The reference point for the plotting"> | |
| 139 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> | |
| 140 <option value="TES">end of region (e.g. TES)</option> | |
| 141 <option value="center">center of region</option> | |
| 142 </param> | |
| 143 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" | |
| 144 label="Discard any values after the region end" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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145 help="This is useful to visualize the region end when not using the |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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146 scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/> |
| 61 | 147 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" |
| 148 label="Distance upstream of the start site of the regions defined in the region file" | |
| 149 help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/> | |
| 150 <param name="afterRegionStartLength" type="integer" value="1000" min="1" | |
| 151 label="Distance downstream of the end site of the given regions" | |
| 152 help="If the regions are genes, this would be the distance downstream of the transcription end site. (--afterRegionStartLength)"/> | |
| 153 </when> | |
| 154 </conditional> | |
| 155 | |
| 156 <expand macro="input_graphic_output_settings"> | |
| 157 <expand macro="input_save_matrix_values" /> | |
| 158 </expand> | |
| 159 | |
| 160 <conditional name="advancedOpt" > | |
| 161 <param name="showAdvancedOpt" type="select" label="Show advanced options" > | |
| 162 <option value="no" selected="true">no</option> | |
| 163 <option value="yes">yes</option> | |
| 164 </param> | |
| 165 <when value="no" /> | |
| 166 <when value="yes"> | |
| 167 <param name="binSize" type="integer" value="10" min="1" | |
| 168 label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length" | |
| 169 help="(--binSize)"/> | |
| 170 <param name="sortRegions" type="select" label="Sort regions" | |
| 171 help="Whether the output file should present the regions sorted."> | |
| 172 <option value="no" selected="true">no ordering</option> | |
| 173 <option value="descend">descending order</option> | |
| 174 <option value="ascend">ascending order</option> | |
| 175 </param> | |
| 176 | |
| 177 <param name="sortUsing" type="select" label="Method used for sorting" | |
| 178 help="The value is computed for each row. (--sortUsing)" > | |
| 179 <option value="mean" selected="true">mean</option> | |
| 180 <option value="median">median</option> | |
| 181 <option value="min">min</option> | |
| 182 <option value="max">max</option> | |
| 183 <option value="sum">sum</option> | |
| 184 <option value="region_length">region length</option> | |
| 185 </param> | |
| 186 | |
| 187 <param name="averageTypeBins" type="select" | |
| 188 label="Define the type of statistic that should be displayed." | |
| 189 help="The value is computed for each bin. (--averageTypeBins)"> | |
| 190 <option value="mean" selected="true">mean</option> | |
| 191 <option value="median">median</option> | |
| 192 <option value="min">min</option> | |
| 193 <option value="max">max</option> | |
| 194 <option value="sum">sum</option> | |
| 195 <option value="std">std</option> | |
| 196 </param> | |
| 197 | |
| 198 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" | |
| 199 label="Indicate missing data as zero" | |
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200 help="Set to "yes", if missing data should be indicated as zeros. |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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201 Default is to ignore such cases which will be depicted as black areas in the |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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202 heatmap. (see "Missing data color" options of the heatmapper for additional options). |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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203 (--missingDataAsZero)"/> |
| 61 | 204 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" |
| 205 label="Skip zeros" | |
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206 help="Whether regions with only scores of zero should be included or not. |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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207 Default is to include them. (--skipZeros)"/> |
| 61 | 208 <param name="minThreshold" type="float" optional="True" |
| 209 label="Minimum threshold" | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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210 help="Any region containing a value that is equal or less than this numeric |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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211 value will be skipped. This is useful to skip, for example, genes where the |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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212 read count is zero for any of the bins. This could be the result of |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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213 unmappable areas and can bias the overall results. (--minThreshold)"/> |
| 61 | 214 <param name="maxThreshold" type="float" optional="True" |
| 215 label="Maximum threshold" | |
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216 help="Any region containing a value that is equal or higher that this |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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217 numeric value will be skipped. The max threshold is useful to skip those |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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218 few regions with very high read counts (e.g. major satellites) that may |
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9bee2c86eeb1
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty
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219 bias the average values. (--maxThreshold)"/> |
| 61 | 220 <param name="scale" type="float" optional="True" label="Scaling factor" |
| 221 help="If set, all values are multiplied by this number. (--scale)"/> | |
| 222 </when> | |
| 223 </conditional> | |
| 224 </inputs> | |
| 225 <outputs> | |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
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226 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> |
| 61 | 227 <expand macro="output_graphic_outputs" /> |
| 228 <expand macro="output_save_matrix_values" /> | |
| 229 </outputs> | |
| 230 <!-- | |
| 231 computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 | |
| 232 --> | |
| 233 <tests> | |
| 234 <test> | |
| 235 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" /> | |
| 236 <param name="scoreFile" value="bamCoverage_result4.bw" ftype="bigwig" /> | |
| 237 <param name="showAdvancedOpt" value="yes" /> | |
| 238 <param name="mode_select" value="reference-point" /> | |
| 239 <param name="binSize" value="10" /> | |
| 240 <param name="sortUsing" value="sum" /> | |
| 241 <param name="averageTypeBins" value="sum" /> | |
| 242 <param name="missingDataAsZero" value="True" /> | |
| 243 <param name="beforeRegionStartLength" value="10" /> | |
| 244 <param name="afterRegionStartLength" value="10" /> | |
|
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245 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> |
| 61 | 246 </test> |
| 247 <test> | |
| 248 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> | |
| 249 <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" /> | |
| 250 <param name="showAdvancedOpt" value="yes" /> | |
| 251 <param name="mode_select" value="reference-point" /> | |
| 252 <param name="binSize" value="10" /> | |
| 253 <param name="beforeRegionStartLength" value="10" /> | |
| 254 <param name="afterRegionStartLength" value="10" /> | |
|
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255 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> |
| 61 | 256 </test> |
| 257 </tests> | |
| 258 <help> | |
| 259 <![CDATA[ | |
| 260 **What it does** | |
| 261 | |
| 262 This tool prepares an intermediary file (a gzipped table of values) | |
| 263 that contains scores associated with genomic regions that can be used | |
| 264 afterwards to plot a heatmap or a profile. | |
| 265 | |
| 266 Genomic regions can really be anything - genes, parts of genes, ChIP-seq | |
| 267 peaks, favorite genome regions... as long as you provide a proper file | |
| 268 in BED or INTERVAL format. If you would like to compare different groups of regions | |
| 269 (i.e. genes from chromosome 2 and 3), you can supply more than 1 BED file, one for each group. | |
| 270 | |
| 271 computeMatrix can also be used to filter and sort | |
| 272 regions according to their score by making use of its advanced output options. | |
| 273 | |
| 274 | |
| 275 .. image:: $PATH_TO_IMAGES/flowChart_computeMatrixetc.png | |
| 276 :alt: Relationship between computeMatrix, heatmapper and profiler | |
| 277 | |
| 278 | |
| 279 You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix | |
| 280 | |
| 281 | |
| 282 ----- | |
| 283 | |
| 284 @REFERENCES@ | |
| 285 ]]> | |
| 286 </help> | |
| 287 <expand macro="citations" /> | |
| 288 </tool> |