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1 <tool name="Heatmap" id="ceas_heatmapr" version="0.1.0">
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2 <description>Draw the scores heatmap near a given interval set and use k-means to cluster the intervals</description>
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3 <macros>
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4 <import>ceas_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_bx" />
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7 <command>
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1
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8 #set $wfiles = str($wfile)
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0
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9 #set $ttitle = "\""+str($title)+"\""
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10 #set $txlabel = "\""+str($xlabel)+"\""
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11 #set $tylabel = "\""+str($ylabel)+"\""
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12 #for $m in $more
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13 #set $wfiles = $wfiles + "," + str($m.wfile)
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14 ###set $ttitle = $ttitle + ",\"" + str($m.title)+"\""
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15 #set $txlabel = $txlabel + ",\"" + str($m.xlabel)+"\""
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16 #set $tylabel = $tylabel + ",\"" + str($m.ylabel)+"\""
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17 #end for
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18 #set $advparam = " --title="+str($ttitle)+" --subtitle="+str($txlabel)+" --y_label="+str($tylabel)
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19
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20 #if $methodadvopt.methodadvopt_select == "kmeans"
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21 #set $methodopt = " --method="+str($methodadvopt.methodadvopt_select)+" -k "+str($methodadvopt.kmeans)+" --k_wigindex="+str($methodadvopt.k_wigindex)
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22 #else if $methodadvopt.methodadvopt_select == "none"
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23 #set $methodopt = " --method="+str($methodadvopt.methodadvopt_select)
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24 #else
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25 #set $methodopt = " --method="+str($methodadvopt.methodadvopt_select)+" --s_wigindex="+str($methodadvopt.s_wigindex)
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26 #end if
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27
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28 #if $advopt.advopt_select == "yes"
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29 #set $advparam = $advparam+" -s "+str($advopt.saturation)+" --upstream="+str($advopt.upstrm)+" --downstream="+str($advopt.dnstrm)+" --pf-res="+str($advopt.step)+" --fontsize="+str($advopt.fontsize)+" --col="+str($advopt.colors)+" --pic_width="+str($advopt.pic_width)+" --pic_height="+str($advopt.pic_height)+" "+str($advopt.horizontal_line)+" "+str($advopt.vertical_line)+" "+str($advopt.dir)+" "+str($advopt.set_seed)
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30
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31 #if $advopt.zmax.value
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32 #set $advparam = $advparam+" --zmax="+str($advopt.zmax)
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33 #end if
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34 #if $advopt.zmin.value
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35 #set $advparam = $advparam+" --zmin="+str($advopt.zmin)
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36 #end if
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37 #else
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38 #set $advparam = " "
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39 #end if
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40 ##
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41 heatmapr -b "$bfile" -w "$wfiles"
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42 #if $wfile.extension == "wig"
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43 --wig_format="wig"
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44 #elif $wfile.extension == "bigwig"
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45 --wig_format="bigwig"
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46 #end if
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47 --name=$name $methodopt $advparam &> $log &&
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48 Rscript output_kmeans.r
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49 </command>
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50 <inputs>
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51 <param name="name" type="hidden" value="output"/>
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52 <param format="bed" name="bfile" type="data" label="BED file(center will be aligned, 100,000 lines max)" />
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53 <param format="wig,bigwig" name="wfile" type="data" label="wig / bigwig file" />
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54 <param name="title" type="text" label="Title for the whole heatmap plot" value="Heatmap" />
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55 <param name="xlabel" type="text" label="Subtitle for heatmap plot" value="subtitle" />
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56 <param name="ylabel" type="text" label="Y-label for heatmap plot" value="Y-label" />
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57 <repeat name="more" title="More wig / bigwig files">
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58 <param format="wig,bigwig" name="wfile" type="data" label="WIGGLE file" />
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59 <param name="xlabel" type="text" label="Subtitle for heatmap plot" value="subtitle" />
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60 <param name="ylabel" type="text" label="Y-label for heatmap plot" value="Y-label" />
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61 </repeat>
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62 <conditional name="methodadvopt">
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63 <param name="methodadvopt_select" type="select" label="choose sort/clustering method">
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64 <option value="kmeans">cluster - kmeans</option>
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65 <option value="median">only sort - median</option>
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66 <option value="maximum">only sort - maximun</option>
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67 <option value="mean">only sort - mean</option>
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68 <option value="none">none - keep original order of bed.</option>
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69 </param>
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70 <when value="kmeans">
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71 <param name="kmeans" type="integer" label="K-means number" value="5">
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72 <validator type="in_range" max="10" min="3" message="K-means is out of range, K-means has to be between 3 to 10" /></param>
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73 <param name="k_wigindex" type="text" label="use which wigs to calc kmeans. input 'all' or sth like '1,2,4' (use the 1st, 2nd and 4th wig.)" value="all" />
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74 </when>
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75 <when value="median">
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76 <param name="s_wigindex" type="integer" label="key wig file for sorting" value="1" />
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77 </when>
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78 <when value="maximum">
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79 <param name="s_wigindex" type="integer" label="key wig file for sorting" value="1" />
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80 </when>
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81 <when value="mean">
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82 <param name="s_wigindex" type="integer" label="key wig file for sorting" value="1" />
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83 </when>
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84 </conditional>
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85 <conditional name="advopt">
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86 <param name="advopt_select" type="select" label="Advanced Options">
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87 <option value="no">No</option>
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88 <option value="yes">Yes</option>
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89 </param>
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90 <when value="yes">
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91 <param name="step" type="integer" label="Step" value="10">
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92 <validator type="in_range" max="1000" min="5" message="step is out of range, step has to be between 5 to 1000" />
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93 </param>
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94 <param name="saturation" type="float" label="Saturation" value="0.01" />
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95 <param name="upstrm" type="integer" label="Upstream" value="500">
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96 <validator type="in_range" max="10000" min="100" message="Upstream is out of range, Upstream has to be between 100 to 10000" />
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97 </param>
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98 <param name="dnstrm" type="integer" label="Downstream" value="500">
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99 <validator type="in_range" max="10000" min="100" message="Downstream is out of range, Downstream has to be between 100 to 10000" />
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100 </param>
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101 <param name="fontsize" type="integer" label="Image fontsize. (better not change)" value="1" />
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102 <param name="colors" type="text" size="100" label="colorRamp for the legend of heatmap, from low value to high, use ','to split" value="053061,2166AC,4393C3,92C5DE,D1E5F0,F7F7F7,FDDBC7,F4A582,D6604D,B2182B,67001F" />
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103 <param name="pic_width" type="integer" label="Heatmap width" value="1920">
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104 <validator type="in_range" max="16000" min="1600" message="Heatmap wodth is out of range, width has to be between 1600 to 16000" />
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105 </param>
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106 <param name="pic_height" type="integer" label="Heatmap height" value="1440">
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107 <validator type="in_range" max="12000" min="1200" message="Heatmap height is out of range, height has to be between 1200 to 12000" />
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108 </param>
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109 <param name="zmin" type="text" label="minimum value in image" />
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110 <param name="zmax" type="text" label="maximum value in image" />
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111 <param name="horizontal_line" type="boolean" label="Plot classified lines?" checked="no" truevalue="-z" falsevalue=" " />
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112 <param name="vertical_line" type="boolean" label="Plot vertical line?" checked="no" truevalue="-v" falsevalue=" " />
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113 <param name="dir" type="boolean" label="consider the direction (+/-) while profiling" checked="no" truevalue="--dir" falsevalue=" " />
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114 <param name="set_seed" type="boolean" label="Set seed to make result reproducible (for developers)" checked="no" truevalue="--set-seed" falsevalue=" " />
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115 </when>
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116 <when value="no" />
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117 </conditional>
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118 </inputs>
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119 <outputs>
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120 <data format="png" name="outputpng" label="Heatmap image" from_work_dir="output_r.heatmap.png"/>
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121 <data format="txt" name="outputr" label="Heatmapr R script" from_work_dir="output_kmeans.r"/>
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122 <data format="tabular" name="outputbed" label="Heatmap k-means classified regions" from_work_dir="output_peak_classid"/>
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123 <data format="txt" name="log" label="Heatmap log" />
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124 </outputs>
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125 <expand macro="stdio" />
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126 <tests>
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127 <test>
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128 <param name="wfile" value="treatment.wig" />
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129 <param name="bfile" value="peak.bed" />
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130 <param name="title" value="title" />
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131 <param name="xlabel" value="xlabel" />
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132 <param name="ylabel" value="ylabel" />
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133 <param name="methodadvopt_select" value="kmeans" />
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134 <param name="kmeans" value="5" />
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135 <param name="advopt_select" value="yes" />
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136 <param name="k_wigindex" value="1" />
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137 <param name="step" value="10" />
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138 <param name="upstrm" value="500" />
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139 <param name="dnstrm" value="400" />
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140 <param name="fontsize" value="2" />
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141 <param name="colors" value="053061,2166AC,4393C3,92C5DE,D1E5F0,F7F7F7,FDDBC7,F4A582,D6604D,B2182B,67001F" />
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142 <param name="zmin" value="" />
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143 <param name="zmax" value="" />
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144 <param name="pic_width" value="1600" />
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145 <param name="pic_height" value="1200" />
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146 <param name="horizontal_line" value="-z" />
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147 <param name="vertical_line" value="-v" />
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148 <param name="dir" value=" " />
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149 <param name="set_seed" value="--set-seed" />
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150 <output name="outputbed">
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151 <assert_contents>
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152 <has_text_matching expression="1\tchr19\t58470227\t58470701\tMACS_peak_9625\t113.34" />
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153 </assert_contents>
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154 </output>
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155 </test>
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156 </tests>
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157 <help>
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158 This tool draws the scores heatmap near a given interval set..It's
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159 based on sitrpro script in Hyunjin Shin's library. Original code is
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160 written by Jian Ma. It uses
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161 R module for kmeans clustering and draw the heatmap.
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162
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163 .. class:: warningmark
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164
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165 **NEED IMPROVEMENT**
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166
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167 -----
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168
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169 **Parameters**
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170
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171 - **BED file** contains the regions to extract the scores from WIGGLE
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172 - **K-means (Advanced)** defines the number of classes in k-means
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173 clustering.
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174 files.
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175 - **WIGGLE file** contains the scores for heatmap.
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176 - **More WIGGLE file** click the *Add new More WIGGLE files* to add
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177 more. All the heatmap for the WIGGLE files will be aligned and
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178 clutered together.
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179 - **Advanced Options** to turn on advanced settings. You will lose
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180 advanced settings and go back to default parameters when you choose
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181 'No'.
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182 - **Upstream/Downstream (Advanced)** size around regions in BED file.
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183 - **Step (Advanced)** is the profiling resolution in bps.
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184 - **Saturation** before the script use the score data to draw heatmap,
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185 it will saturate the data to a narrow scale. For example, if you set
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186 the option to 0.1, The data smaller than 10% of the data or bigger
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187 than 90% of the data will be saturated to 10% or 90% of the data.
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188 - **col_low/col_high** is the color of legend for images.
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189 - **pic_width/pic_height** is the size of heatmap image.
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190 - **zmin/zmax** is the max value and min value for the legend bar.
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191 - **horizontal_line** lines in black to separate the clusters.
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192
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193 -----
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194
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195 **Outputs**
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196
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197 - *PNG file* is the heatmap image
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198 - *clustering result file* Contain the clustering results from the
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199 tool. The 'Score' column (5th column) contains the cluster indices.
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200 - *Log* for job log. If you see errors, please attached this in
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201 the bug report
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202
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203 </help>
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204
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205 </tool>
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