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1 <tool id="corrcoverage" name="correlation" version="0.5.0">
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2 <description>of coverage</description>
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3 <command interpreter="sh">
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4 mkCorr.sh
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5 #echo ','.join(map(lambda (x): x.get('file').__str__(), $files))
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6
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7 #echo ','.join(map(lambda (x): "\""+(x.get('file').name if x.get('cname').__str__() == "" else x.get('cname').__str__())+"\"", $files))
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8
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9 #echo ','.join(map(lambda (x): x.get('file').ext, $files))
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10
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11 $plotout
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12
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13 $matout
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14
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15 "$name"
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16 </command>
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17
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18 <inputs>
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19 <param name="name" type="text" label="experiment name" value="NA"></param>
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20 <repeat name="files" title="input files" min="2">
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21 <param name="file" format="bed,bigWig" type="data" label="file" help="input file for correlation"/>
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22 <param name="cname" format="text" type="text" label="optional name" value="" help="name for condition"/>
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23 </repeat>
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24
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25 </inputs>
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26
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27 <outputs>
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28 <data format="pdf" name="plotout" label="#if str($name) == 'NA' then $on_string else $name# correlation plot"/>
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29 <data format="tabular" name="matout" label="#if str($name) == 'NA' then $on_string else $name# correlation matrix"/>
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30 </outputs>
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31
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32
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33 <help>
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34 Correlate Coverage:
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35 ===================
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36
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37 Takes at least two files and calculates the correlation of the coverage. The correlation
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38 is calculated by using the union of all the regions that are covered in the tracks.
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39
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40 Requirements:
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41 -------------
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42
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43 At least two files of 6 column bed, wig(?) or bigWig format
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44
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45 Outputs:
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46 --------
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47 Plot of pearson clustering of correlation coefficient.
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48 Matrix of pearson correlation coefficients.
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49
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50 TODO:
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51 -----
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52 Add mappability track option
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53 Add bam as input
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54 </help>
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55 </tool>
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56
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57
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58
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59
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