Mercurial > repos > xuebing > sharplabtool
comparison mytools/cdf.xml @ 9:87eb5c5ddfe9
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 20:01:43 -0500 |
| parents | f0dc65e7f6c0 |
| children |
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| 8:361ec1c0479d | 9:87eb5c5ddfe9 |
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| 1 <tool id="cdf" name="CDF"> | |
| 2 <description>plot of multiple numeric columns</description> | |
| 3 <command>cat $script_file | R --vanilla --slave > $out_log </command> | |
| 4 <inputs> | |
| 5 <param name="title" type="text" value="CDF plot" size="30" label="Plot title"/> | |
| 6 <param name="xlabel" type="text" value="value" size="30" label="xlabel"/> | |
| 7 <param name="log" label="log2 transform the data" type="boolean" truevalue="log" falsevalue="none" checked="False"/> | |
| 8 <param name="zero" label="remove zero" type="boolean" truevalue="zero" falsevalue="none" checked="False"/> | |
| 9 <param name="legendloc" type="select" label="legend location on CDF plot" > | |
| 10 <option value="bottomright" selected="true">bottomright</option> | |
| 11 <option value="bottomleft">bottomleft</option> | |
| 12 <option value="bottom">bottom</option> | |
| 13 <option value="left">left</option> | |
| 14 <option value="topleft">topleft</option> | |
| 15 <option value="top">top</option> | |
| 16 <option value="topright">topright</option> | |
| 17 <option value="right">right</option> | |
| 18 <option value="center">center</option> | |
| 19 </param> | |
| 20 <repeat name="series" title="sample"> | |
| 21 <param name="label" type="text" value="" size="30" label="data label"/> | |
| 22 <param name="input" type="data" format="tabular" label="dataset"/> | |
| 23 <param name="column" type="integer" value="2" label="column number (-1 for last column)"/> | |
| 24 </repeat> | |
| 25 | |
| 26 </inputs> | |
| 27 | |
| 28 <configfiles> | |
| 29 <configfile name="script_file"> | |
| 30 ## Setup R error handling to go to stderr | |
| 31 options(warn=-1) | |
| 32 source("/Users/xuebing/galaxy-dist/tools/mytools/cdf.r") | |
| 33 uselog = as.character("${log}") | |
| 34 zero = as.character("${zero}") | |
| 35 title = as.character("${title}") | |
| 36 xlabel = as.character("${xlabel}") | |
| 37 if (uselog=='log'){ | |
| 38 xlabel = paste('log2',xlabel) | |
| 39 } | |
| 40 | |
| 41 labels = character(0) | |
| 42 x = list() | |
| 43 #for $i, $s in enumerate( $series ) | |
| 44 labels = c(labels,"${s.label.value}") | |
| 45 x0 = read.table( "${s.input.file_name}" ,sep='\t') | |
| 46 col = ${s.column.value} | |
| 47 if (col == -1) {col = ncol(x0)} | |
| 48 x0 = x0[,col] | |
| 49 if (zero == 'zero'){ | |
| 50 x0 = x0[x0 != 0] | |
| 51 } | |
| 52 if (uselog=='log'){ | |
| 53 x0=log2(1+x0) | |
| 54 } | |
| 55 print("${s.label.value}") | |
| 56 summary(x0) | |
| 57 x[[$i+1]] = x0 | |
| 58 #end for | |
| 59 pdf("${out_file}") | |
| 60 mycdf(x,title,labels,"${legendloc}",xlabel,'') | |
| 61 dev.off() | |
| 62 </configfile> | |
| 63 </configfiles> | |
| 64 | |
| 65 <outputs> | |
| 66 <data format="txt" name="out_log" label="${tool.name} on ${on_string}: (log)" /> | |
| 67 <data format="pdf" name="out_file" label="${tool.name} on ${on_string}: (plot)" /> | |
| 68 </outputs> | |
| 69 | |
| 70 <help> | |
| 71 | |
| 72 .. class:: infomark | |
| 73 | |
| 74 This tool generate barplot and CDF plot comparing multiple numeric columns in different files. | |
| 75 | |
| 76 | |
| 77 </help> | |
| 78 </tool> |