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1 <tool id="knitrtest" name="testing knitr" version="0.0.1">
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2 Additional info: wrapper compatible with versions .....
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3 <description>
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4 for R scripts plugins.
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5 </description>
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6
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7 <requirements>
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8 <requirement type="package" version="2.12">biocbasics</requirement>
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9 <requirement type="package" version="3.0.1">package_r3</requirement>
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10 </requirements>
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11
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12 <command interpreter="sh">
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13 /usr/local/bin/R CMD BATCH ${runme}
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14 </command>
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15
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16 <inputs>
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17 <param format="tabular" name="counttable" type="data" label="Count table" help="Count table generated by HTSeq-count" />
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18 <param name="title" type="text" value="edgeR" size="80" label="Title for job outputs" help="Supply a meaningful name here to remind you what the outputs contain">
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19 <sanitizer invalid_char="">
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20 <valid initial="string.letters,string.digits"><add value="_" /> </valid>
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21 </sanitizer>
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22 </param>
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23 <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
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24 <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="counttable" numerical="True"
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25 multiple="true" use_header_names="true" size="120" display="checkboxes">
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26 <validator type="no_options" message="Please select at least one column."/>
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27 </param>
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28 <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
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29 <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="counttable" numerical="True"
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30 multiple="true" use_header_names="true" size="120" display="checkboxes" optional="true">
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31 </param>
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32 <param name="subjectids" type="text" optional="true" size="120" value = ""
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33 label="IF SUBJECTS NOT ALL INDEPENDENT! Enter integers to indicate sample pairing for every column in count table"
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34 help="Leave blank if no pairing, but eg if data from sample id A99 is in columns 2,4 and id C21 is in 3,5 then enter '1,2,1,2'">
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35 <sanitizer>
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36 <valid initial="string.digits"><add value="," /> </valid>
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37 </sanitizer>
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38 </param>
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39 <param name="fQ" type="float" value="0.3" size="5" label="Non-differential contig count quantile threshold - zero to analyze all non-zero read count contigs"
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40 help="May be a good or a bad idea depending on the biology and the question. EG 0.3 = sparsest 30% of contigs with at least one read are removed before analysis"/>
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41 <param name="useNDF" type="boolean" truevalue="T" checked='false' falsevalue="" size="1" label="Non differential filter - remove contigs below a threshold (1 per million) for half or more samples"
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42 help="May be a good or a bad idea depending on the biology and the question. This was the old default. Quantile based is available as an alternative"/>
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43 <param name="priordf" type="integer" value="20" size="3" label="prior.df for tagwise dispersion - lower value = more emphasis on each tag's variance. Replaces prior.n and prior.df = prior.n * residual.df"
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44 help="Zero = Use edgeR default. Use a small value to 'smooth' small samples. See edgeR docs and note below"/>
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45 <param name="fdrthresh" type="float" value="0.05" size="5" label="P value threshold for FDR filtering for amily wise error rate control"
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46 help="Conventional default value of 0.05 recommended"/>
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47 <param name="fdrtype" type="select" label="FDR (Type II error) control method"
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48 help="Use fdr or bh typically to control for the number of tests in a reliable way">
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49 <option value="fdr" selected="true">fdr</option>
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50 <option value="BH">Benjamini Hochberg</option>
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51 <option value="BY">Benjamini Yukateli</option>
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52 <option value="bonferroni">Bonferroni</option>
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53 <option value="hochberg">Hochberg</option>
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54 <option value="holm">Holm</option>
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55 <option value="hommel">Hommel</option>
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56 <option value="none">no control for multiple tests</option>
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57 </param>
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58 </inputs>
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59
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60 <outputs>
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61 <data format="tabular" name="outtab" label="${title}.xls"/>
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62 <data format="html" name="html_file" label="${title}.html"/>
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63 </outputs>
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64
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65 <configfiles>
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66 <configfile name="inputscript">
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67 Differential expression analysis
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68 ================================
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69
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70 Loading the R environment
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71 ```{r}
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72 # Original edgeR code by: S.Lunke and A.Kaspi
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73 reallybig = log10(.Machine\$double.xmax)
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74 reallysmall = log10(.Machine\$double.xmin)
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75 library('stringr')
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76 library('gplots')
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77 library('DESeq')
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78 library('edgeR')
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79 ```
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80
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81 Reading count table from parameters
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82 ```{r}
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83 filename="$counttable"
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84 raw_counts = read.csv(filename, header=TRUE, stringsAsFactors=F)
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85 ```
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86
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87 And printing the count table
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88 ```{r}
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89 head(raw_counts)
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90 ```
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91
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92 End of markdown script.
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93 </configfile>
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94 <configfile name="runme">
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95 require(knitr)
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96 require(markdown)
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97 knit("${inputscript}", "test.md")
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98 markdownToHTML("test.md", "${html_file}")
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99 </configfile>
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100 </configfiles>
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101
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102 <tests>
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103 </tests>
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104
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105 <help>
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106 **knitr test**
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107 Testing whether two config files can be nested.
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108 </help>
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109 </tool>
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110
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