Mercurial > repos > bgruening > deeptools_compute_matrix
annotate computeMatrix.xml @ 21:c1bc6406b3bb draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a
| author | bgruening |
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| date | Wed, 22 Aug 2018 17:28:37 -0400 |
| parents | fb9cf9c97ec4 |
| children | f305afa8ff0d |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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1 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0"> |
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2 <description>prepares data for plotting a heatmap or a profile of given regions</description> |
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3 <macros> |
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4 <token name="@BINARY@">computeMatrix</token> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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5 <import>deepTools_macros.xml</import> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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6 </macros> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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7 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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8 <command> |
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9 <![CDATA[ |
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10 @multiple_input_bigwigs@ |
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11 |
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12 #set bed_files=[] |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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13 #for $counter, $rf, in enumerate($regionsFiles): |
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14 #set identifier = re.sub('[^\s\w\-]', '_', str($rf.regionsFile.element_identifier)) |
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15 ln -f -s '${rf.regionsFile}' '${identifier}_${counter}.bed' && |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
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16 #silent $bed_files.append('%s_%s.bed' % ($identifier, $counter)) |
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17 #end for |
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18 |
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19 @BINARY@ |
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20 |
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21 $mode.mode_select |
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22 --regionsFileName '#echo "' '".join($bed_files)#' |
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23 |
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24 --scoreFileName #echo ' '.join($files)# |
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25 |
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26 --outFileName '$outFileName' |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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27 |
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28 @THREADS@ |
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29 |
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30 #if $output.showOutputSettings == "yes" |
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31 #if $output.saveMatrix: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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32 --outFileNameMatrix '$outFileNameMatrix' |
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33 #end if |
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34 |
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35 #if $output.saveSortedRegions: |
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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
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36 --outFileSortedRegions '$outFileSortedRegions' |
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37 #end if |
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38 #end if |
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39 |
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40 #if $mode.mode_select == "reference-point": |
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41 --referencePoint $mode.referencePoint |
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42 $mode.nanAfterEnd |
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43 --beforeRegionStartLength $mode.beforeRegionStartLength |
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44 --afterRegionStartLength $mode.afterRegionStartLength |
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45 #else |
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46 --regionBodyLength $mode.regionBodyLength |
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47 #if $mode.regionStartLength.regionStartLength_select == "yes": |
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48 --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength |
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49 --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength |
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50 |
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51 --unscaled5prime $mode.regionStartLength.unscaled5prime |
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52 --unscaled3prime $mode.regionStartLength.unscaled3prime |
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53 |
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54 #end if |
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56 #end if |
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57 |
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58 #if $advancedOpt.showAdvancedOpt == "yes": |
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59 --sortRegions '$advancedOpt.sortRegions' |
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60 --sortUsing '$advancedOpt.sortUsing' |
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61 --averageTypeBins '$advancedOpt.averageTypeBins' |
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62 $advancedOpt.skipZeros |
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63 $advancedOpt.missingDataAsZero |
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64 --binSize $advancedOpt.binSize |
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65 |
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66 #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '': |
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67 --minThreshold $advancedOpt.minThreshold |
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68 #end if |
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69 #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '': |
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70 --maxThreshold $advancedOpt.maxThreshold |
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71 #end if |
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72 #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '': |
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73 --scale $advancedOpt.scale |
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74 #end if |
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75 #if $advancedOpt.samplesLabel is not None and str($advancedOpt.samplesLabel) != '': |
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76 --samplesLabel $advancedOpt.samplesLabel |
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77 #end if |
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78 |
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79 @ADVANCED_OPTS_GTF@ |
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80 |
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81 @blacklist@ |
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82 |
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83 #end if |
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84 ]]> |
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85 </command> |
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86 <inputs> |
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87 |
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88 <repeat name="regionsFiles" title="Select regions" min="1"> |
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89 <param name="regionsFile" format="bed,gtf" type="data" label="Regions to plot" |
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90 help="File, in BED format, containing the regions to plot."/> |
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91 </repeat> |
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92 |
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93 <expand macro="multiple_input_bigwigs" MIN="1" LABEL="Score file" TITLE="Score files"/> |
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94 |
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95 <conditional name="mode" > |
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96 <param name="mode_select" type="select" |
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97 label="computeMatrix has two main output options" |
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98 help="In the scale-regions mode, all regions in the BED file are |
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99 stretched or shrunken to the same length (in bases) that is indicated |
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100 by the user. Reference-point refers to a position within the BED |
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101 regions (start or end of each region). In the reference-point mode only |
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102 those genomic positions before (upstream) and/or after (downstream) |
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103 the reference point will be considered."> |
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104 <option value="scale-regions" selected="true">scale-regions</option> |
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105 <option value="reference-point">reference-point</option> |
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106 </param> |
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107 |
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108 <when value="scale-regions" > |
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109 <param argument="--regionBodyLength" type="integer" value="500" |
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110 label="Distance in bases to which all regions are going to be fit" help=""/> |
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111 <conditional name="regionStartLength"> |
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112 <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions"> |
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113 <option value="no" selected="true">no</option> |
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114 <option value="yes">yes</option> |
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115 </param> |
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116 <when value="no" /> |
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117 <when value="yes"> |
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118 <param argument="--beforeRegionStartLength" type="integer" value="1000" min="1" |
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119 label="Distance upstream of the region start position" |
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120 help="If the regions are genes, this would be the |
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121 distance upstream of the transcription start site."/> |
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122 <param argument="--afterRegionStartLength" type="integer" value="1000" min="1" |
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123 label="Distance downstream of the region end position" |
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124 help="If the regions are genes, this would be the |
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125 distance downstream of the transcription end site."/> |
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126 <param argument="--unscaled5prime" type="integer" min="0" value="0" |
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127 label="Number of bases within the gene body at the 5-prime end to exclude from scaling." |
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128 help="By default, each region is scaled to a given length (see the --regionBodyLength |
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129 option). In some cases it is useful to look at unscaled signals around region boundaries, so this |
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130 setting specifies the number of unscaled bases on the 5-prime end of each boundary." /> |
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131 <param argument="--unscaled3prime" type="integer" min="0" value="0" |
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132 label="Number of bases within the gene body at the 3-prime end to exclude from scaling." |
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133 help="As with --unscaled5prime, but for the 3-prime end." /> |
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134 </when> |
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135 </conditional> |
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136 </when> |
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137 <when value="reference-point"> |
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138 <param name="referencePoint" type="select" label="The reference point for the plotting"> |
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139 <option value="TSS" selected="true">beginning of region (e.g. TSS)</option> |
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140 <option value="TES">end of region (e.g. TES)</option> |
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141 <option value="center">center of region</option> |
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142 </param> |
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143 <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" |
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144 label="Discard any values after the region end" |
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145 help="This is useful to visualize the region end when not using the |
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146 scale-regions mode and when the reference-point is set to the TSS. (--nanAfterEnd)"/> |
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147 <param name="beforeRegionStartLength" type="integer" value="1000" min="1" |
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148 label="Distance upstream of the start site of the regions defined in the region file" |
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149 help="If the regions are genes, this would be the distance upstream of the transcription start site. (--beforeRegionStartLength)"/> |
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150 <param name="afterRegionStartLength" type="integer" value="1000" min="1" |
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151 label="Distance downstream of the end site of the given regions" |
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152 help="If the regions are genes, this would be the distance downstream of the transcription end site. (--afterRegionStartLength)"/> |
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153 </when> |
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154 </conditional> |
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155 |
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156 <expand macro="input_graphic_output_settings"> |
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157 <expand macro="input_save_matrix_values" /> |
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158 </expand> |
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159 |
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160 <conditional name="advancedOpt" > |
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161 <param name="showAdvancedOpt" type="select" label="Show advanced options" > |
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162 <option value="no" selected="true">no</option> |
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163 <option value="yes">yes</option> |
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164 </param> |
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165 <when value="no" /> |
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166 <when value="yes"> |
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167 <param name="binSize" type="integer" value="50" min="1" |
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168 label="Length, in bases, of non-overlapping bins used for averaging the score over the regions length" |
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169 help="(--binSize)"/> |
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170 |
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171 <expand macro="sortRegionsComputeMatrix" /> |
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172 <expand macro="sortUsing" /> |
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173 |
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174 <param name="averageTypeBins" type="select" |
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175 label="Define the type of statistic that should be displayed." |
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176 help="The value is computed for each bin. (--averageTypeBins)"> |
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177 <option value="mean" selected="true">mean</option> |
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178 <option value="median">median</option> |
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179 <option value="min">min</option> |
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180 <option value="max">max</option> |
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181 <option value="sum">sum</option> |
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182 <option value="std">std</option> |
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183 </param> |
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184 |
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185 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" checked="False" |
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186 label="Convert missing values to 0?" |
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187 help="If set to 'yes', missing values (NAs) are converted |
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188 to 0. If you want to use clustering with plotHeatmap |
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189 or plotProfile, set this to 'yes'. |
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190 The default is to ignore missing values, which will be |
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191 depicted as black areas once a heatmap is created. |
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192 (--missingDataAsZero)" /> |
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193 |
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194 <expand macro="skipZeros" /> |
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195 |
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196 <param name="minThreshold" type="float" optional="True" |
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197 label="Minimum threshold" |
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198 help="Any region containing a value that is equal or less than this numeric |
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199 value will be skipped. This is useful to skip, for example, genes where the |
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200 read count is zero for any of the bins which could be the result of |
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201 unmappable areas and can bias the overall results. (--minThreshold)"/> |
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202 <param name="maxThreshold" type="float" optional="True" |
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203 label="Maximum threshold" |
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204 help="Any region containing a value that is equal or higher that this |
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205 numeric value will be skipped. The max threshold is useful to skip those |
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206 few regions with very high read counts (e.g. major satellites) that may |
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207 bias the average values. (--maxThreshold)"/> |
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208 <param name="scale" type="float" optional="True" label="Scaling factor" |
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209 help="If set, all values are multiplied by this number. (--scale)"/> |
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210 <param argument="--samplesLabel" type="text" size="30" |
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211 label="Labels for the samples (each bigwig)" |
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212 help="The default is to use the history item label. The sample labels should be separated by |
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213 spaces and quoted if a label itself contains a space E.g. label-1 "label 2""> |
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214 <sanitizer> |
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215 <valid initial="string.printable"> |
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216 </valid> |
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217 </sanitizer> |
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218 </param> |
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219 |
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220 <expand macro="gtf_options" /> |
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221 |
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222 <expand macro="blacklist" /> |
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223 </when> |
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224 </conditional> |
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225 </inputs> |
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226 <outputs> |
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227 <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" /> |
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228 <expand macro="output_graphic_outputs" /> |
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229 <expand macro="output_save_matrix_values" /> |
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230 </outputs> |
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231 <tests> |
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232 <test> |
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233 <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" /> |
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234 <param name="bigwigfiles" value="bamCoverage_result4.bw" ftype="bigwig" /> |
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235 <param name="showAdvancedOpt" value="yes" /> |
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236 <param name="mode_select" value="reference-point" /> |
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237 <param name="binSize" value="10" /> |
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238 <param name="sortUsing" value="sum" /> |
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239 <param name="averageTypeBins" value="sum" /> |
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240 <param name="beforeRegionStartLength" value="10" /> |
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241 <param name="afterRegionStartLength" value="10" /> |
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242 <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> |
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243 </test> |
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244 <test> |
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245 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> |
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246 <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" /> |
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247 <param name="showAdvancedOpt" value="yes" /> |
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248 <param name="mode_select" value="reference-point" /> |
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249 <param name="binSize" value="10" /> |
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250 <param name="beforeRegionStartLength" value="10" /> |
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251 <param name="afterRegionStartLength" value="10" /> |
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252 <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> |
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253 </test> |
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254 <test> |
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255 <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" /> |
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256 <param name="bigwigfiles" value="computeMatrix2.bw" ftype="bigwig" /> |
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257 <param name="showAdvancedOpt" value="yes" /> |
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258 <param name="mode_select" value="scale-regions" /> |
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259 <param name="endLabel" value="END" /> |
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260 <param name="regionStartLength" value="yes" /> |
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261 <output name="outFileName" file="computeMatrix_result3.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" /> |
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262 </test> |
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263 </tests> |
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264 <help> |
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265 <![CDATA[ |
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266 |
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267 What it does |
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268 ---------------- |
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269 |
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270 This tool prepares an intermediate file (a gzipped table of values) |
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271 that contains scores associated with genomic regions. |
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272 The regions can either be scaled to the same size (using the ``scale-regions`` mode) or you can choose the start, end, or center of each region as the focus point for the score calculations. |
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273 For more details, check out the explanation `here <https://deeptools.readthedocs.io/en/latest/content/tools/computeMatrix.html#details>`_. |
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274 |
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275 The intermediate file produced by ``computeMatrix`` is meant to be used with ``plotHeatmap`` and ``plotProfile``. |
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276 See the descriptions of ``plotHeatmap`` and ``plotProfile`` for example plots. |
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277 |
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278 .. image:: $PATH_TO_IMAGES/computeMatrix_overview.png |
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279 :alt: Relationship between computeMatrix, heatmapper and profiler |
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280 :width: 600 |
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281 :height: 418 |
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282 |
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283 ======= |
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284 |
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285 Usage hints |
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286 ------------- |
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287 |
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288 The supplied genomic regions can really be anything - genes, parts of genes, ChIP-seq peaks, favorite genome regions... as long as you provide a proper file |
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289 in BED or INTERVAL format. If you would like to compare different groups of regions (e.g., genes from chromosome 2 and 3), you can supply more than 1 regions file, one for each group by selecting "Insert Select regions". |
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290 |
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291 .. image:: $PATH_TO_IMAGES/computeMatrix_selectRegions.png |
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292 :width: 600 |
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293 :height: 150 |
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294 |
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295 You can select as many score (bigWig) files as you like. Simply use the Shift and/or Command key while clicking on the files of interest. |
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296 |
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297 .. image:: $PATH_TO_IMAGES/computeMatrix_selectScores.png |
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298 :width: 600 |
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299 :height: 136 |
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300 |
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301 The multitude of parameters can seem daunting at first - here are the options that we tend to tune most often: |
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302 |
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303 * ``bin Size`` -- The default value works well most of the time, but if you want to have a more finely grained image, decrease the default value (but not smaller than your bigWig file(s)' bin size). If you want to reduce the computation time, increase it. |
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304 * ``Skip zeros`` -- useful to avoid completely blank lines in the heatmap. |
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305 * ``Convert missing values to 0?`` -- If you want to identify clusters of similar regions in an unsupervised fashion using ``plotHeatmap`` and/or ``plotProfile``, you should definitely set this to 'yes'. |
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306 |
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307 |
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308 Output files |
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309 --------------- |
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310 |
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311 The default output is a **gzipped table of values** that is used by both ``plotHeatmap`` and ``plotProfile``. |
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312 |
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313 The optional output files include a) the **regions after sorting and filtering (if selected)** as they were used to calculate the values for the plotting, and b) the uncompressed table that **underlies the heatmap**. |
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314 |
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315 **TIP:** ``computeMatrix`` can also be used to filter and sort regions according to their score by making use of the "advanced output settings". |
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316 |
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317 .. image:: $PATH_TO_IMAGES/computeMatrix_advancedOutput.png |
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318 :width: 600 |
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319 :height: 189 |
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320 |
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321 .. image:: $PATH_TO_IMAGES/computeMatrix_output.png |
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322 :width: 600 |
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323 :height: 297 |
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324 |
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325 Note that these advanced output options are available for ``plotHeatmap`` and ``plotProfile``, too. |
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326 |
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327 See the following table for the optional output options: |
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328 |
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329 +-----------------------------------+--------------------+-----------------+-----------------+ |
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330 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** | |
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331 +-----------------------------------+--------------------+-----------------+-----------------+ |
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332 | values underlying the heatmap | yes | yes | no | |
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333 +-----------------------------------+--------------------+-----------------+-----------------+ |
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334 | values underlying the profile | no | no | yes | |
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335 +-----------------------------------+--------------------+-----------------+-----------------+ |
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336 | sorted and/or filtered regions | yes | yes | yes | |
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337 +-----------------------------------+--------------------+-----------------+-----------------+ |
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338 |
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339 **More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_. |
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340 |
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341 ----- |
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342 |
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343 @REFERENCES@ |
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344 ]]> |
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345 </help> |
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346 <expand macro="citations" /> |
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347 </tool> |