Mercurial > repos > idot > coverage_correlation
comparison corr.xml @ 0:06cd86f06fb0
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| author | idot |
|---|---|
| date | Sun, 18 Aug 2013 09:42:18 -0400 |
| parents | |
| children | cde608491511 |
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| -1:000000000000 | 0:06cd86f06fb0 |
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| 1 <tool id="corrcoverage" name="correlation" version="0.5.0"> | |
| 2 <description>of coverage</description> | |
| 3 <command interpreter="sh"> | |
| 4 mkCorr.sh | |
| 5 #echo ','.join(map(lambda (x): x.get('file').__str__(), $files)) | |
| 6 | |
| 7 #echo ','.join(map(lambda (x): "\""+(x.get('file').name if x.get('cname').__str__() == "" else x.get('cname').__str__())+"\"", $files)) | |
| 8 | |
| 9 #echo ','.join(map(lambda (x): x.get('file').ext, $files)) | |
| 10 | |
| 11 $plotout | |
| 12 | |
| 13 $matout | |
| 14 | |
| 15 "$name" | |
| 16 </command> | |
| 17 | |
| 18 <inputs> | |
| 19 <param name="name" type="text" label="experiment name" value="NA"></param> | |
| 20 <repeat name="files" title="input files" min="2"> | |
| 21 <param name="file" format="bed,bigWig" type="data" label="file" help="input file for correlation"/> | |
| 22 <param name="cname" format="text" type="text" label="optional name" value="" help="name for condition"/> | |
| 23 </repeat> | |
| 24 | |
| 25 </inputs> | |
| 26 | |
| 27 <outputs> | |
| 28 <data format="pdf" name="plotout" label="#if str($name) == 'NA' then $on_string else $name# correlation plot"/> | |
| 29 <data format="tabular" name="matout" label="#if str($name) == 'NA' then $on_string else $name# correlation matrix"/> | |
| 30 </outputs> | |
| 31 | |
| 32 | |
| 33 <help> | |
| 34 Correlate Coverage: | |
| 35 =================== | |
| 36 | |
| 37 Takes at least two files and calculates the correlation of the coverage. The correlation | |
| 38 is calculated by using the union of all the regions that are covered in the tracks. | |
| 39 | |
| 40 Requirements: | |
| 41 ------------- | |
| 42 | |
| 43 At least two files of 6 column bed, wig(?) or bigWig format | |
| 44 | |
| 45 Outputs: | |
| 46 -------- | |
| 47 Plot of pearson clustering of correlation coefficient. | |
| 48 Matrix of pearson correlation coefficients. | |
| 49 | |
| 50 TODO: | |
| 51 ----- | |
| 52 Add mappability track option | |
| 53 Add bam as input | |
| 54 </help> | |
| 55 </tool> | |
| 56 | |
| 57 | |
| 58 | |
| 59 | |
| 60 |