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11
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1 <tool id="cdf" name="CDF">
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2 <description>plot of multiple numeric columns</description>
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3 <command>cat $script_file | R --vanilla --slave > $out_log </command>
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4 <inputs>
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5 <param name="title" type="text" value="CDF plot" size="30" label="Plot title"/>
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6 <param name="xlabel" type="text" value="value" size="30" label="xlabel"/>
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7 <param name="log" label="log2 transform the data" type="boolean" truevalue="log" falsevalue="none" checked="False"/>
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8 <param name="zero" label="remove zero" type="boolean" truevalue="zero" falsevalue="none" checked="False"/>
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9 <param name="legendloc" type="select" label="legend location on CDF plot" >
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10 <option value="bottomright" selected="true">bottomright</option>
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11 <option value="bottomleft">bottomleft</option>
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12 <option value="bottom">bottom</option>
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13 <option value="left">left</option>
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14 <option value="topleft">topleft</option>
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15 <option value="top">top</option>
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16 <option value="topright">topright</option>
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17 <option value="right">right</option>
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18 <option value="center">center</option>
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19 </param>
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20 <repeat name="series" title="sample">
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21 <param name="label" type="text" value="" size="30" label="data label"/>
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22 <param name="input" type="data" format="tabular" label="dataset"/>
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23 <param name="column" type="integer" value="2" label="column number (-1 for last column)"/>
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24 </repeat>
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25
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26 </inputs>
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27
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28 <configfiles>
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29 <configfile name="script_file">
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30 ## Setup R error handling to go to stderr
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31 options(warn=-1)
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32 source("/Users/xuebing/galaxy-dist/tools/mytools/cdf.r")
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33 uselog = as.character("${log}")
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34 zero = as.character("${zero}")
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35 title = as.character("${title}")
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36 xlabel = as.character("${xlabel}")
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37 if (uselog=='log'){
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38 xlabel = paste('log2',xlabel)
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39 }
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40
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41 labels = character(0)
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42 x = list()
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43 #for $i, $s in enumerate( $series )
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44 labels = c(labels,"${s.label.value}")
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45 x0 = read.table( "${s.input.file_name}" ,sep='\t')
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46 col = ${s.column.value}
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47 if (col == -1) {col = ncol(x0)}
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48 x0 = x0[,col]
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49 if (zero == 'zero'){
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50 x0 = x0[x0 != 0]
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51 }
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52 if (uselog=='log'){
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53 x0=log2(1+x0)
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54 }
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55 print("${s.label.value}")
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56 summary(x0)
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57 x[[$i+1]] = x0
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58 #end for
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59 pdf("${out_file}")
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60 mycdf(x,title,labels,"${legendloc}",xlabel,'')
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61 dev.off()
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62 </configfile>
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63 </configfiles>
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64
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65 <outputs>
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66 <data format="txt" name="out_log" label="${tool.name} on ${on_string}: (log)" />
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67 <data format="pdf" name="out_file" label="${tool.name} on ${on_string}: (plot)" />
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68 </outputs>
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69
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70 <help>
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71
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72 .. class:: infomark
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73
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74 This tool generate barplot and CDF plot comparing multiple numeric columns in different files.
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75
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76
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77 </help>
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78 </tool>
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