Mercurial > repos > yhoogstrate > edger_with_design_matrix

annotate edgeR_Convert_DGE_Table_to_Bedgraph.xml @ 109:dfebd3787276 draft

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author yhoogstrate
date Tue, 01 Sep 2015 04:53:59 -0400
parents a02794bb9073
children f871dff92e7c
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0">
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3 <description>EdgeR's "differentially expressed genes" table to bedgraph(s)</description>
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5 <macros>
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6 <import>edgeR_macros.xml</import>
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7 </macros>
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9 <requirements>
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10 <requirement type="package" version="1.0.0">edger_dge_table_to_bedgraph</requirement>
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11 </requirements>
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13 <command interpreter="python">
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14 edger_dge_table_to_bedgraph
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15 -t $cpm_table
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16 -g $geneset
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18 #if $logfc:
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19 -c3 $logfc
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20 #end if
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22 #if $logcpm:
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23 -c4 $logcpm
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24 #end if
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26 #if $lr:
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27 -c5 $lr
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28 #end if
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30 #if $pvalue:
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31 -c6 $pvalue
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32 #end if
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34 #if $fdr:
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35 -c7 $fdr
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36 #end if
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37 </command>
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39 <inputs>
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40 <param format="tabular" name="cpm_table" type="data" label="'differentially expressed genes'-table as result from EdgeR" help="must have 7 columns of which the 2nd are gene names matching the GTF file" />
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41 <param format="gtf,gff,gff3" name="geneset" type="data" label="Geneset used for estimating expression levels prior to expression analysis" />
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42
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43 <param name="columns" type="select" label="Desired columns" multiple="true" display="checkboxes">
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44 <option value="c3" selected="true">logFC</option>
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45 <option value="c4">logCPM</option>
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46 <option value="c5">LR</option>
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47 <option value="c6">PValue</option>
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48 <option value="c7" selected="true">FDR</option>
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49 </param>
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50 </inputs>
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52 <outputs>
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53 <data format="bedgraph" name="logfc" label="logFC from ${cpm_table.name}">
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54 <filter>"c3" in columns</filter>
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55 </data>
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56
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57 <data format="bedgraph" name="logcpm" label="logCPM from ${cpm_table.name}">
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58 <filter>"c4" in columns</filter>
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59 </data>
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61 <data format="bedgraph" name="lr" label="LR from ${cpm_table.name}">
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62 <filter>"c5" in columns</filter>
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63 </data>
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65 <data format="bedgraph" name="pvalue" label="PValue from ${cpm_table.name}">
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66 <filter>"c6" in columns</filter>
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67 </data>
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68
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69 <data format="bedgraph" name="fdr" label="FDR from ${cpm_table.name}">
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70 <filter>"c7" in columns</filter>
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71 </data>
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72 </outputs>
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73
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74 <tests>
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75 <test>
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76 <param name="cpm_table" value="Convert_DGE_Table_to_Bedgraph/table_01.tabular.txt" />
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77 <param name="geneset" value="Convert_DGE_Table_to_Bedgraph/genes_01.gtf" />
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78
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79 <param name="columns" value="c3,c7" />
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80
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81 <output name="logfc" file="Convert_DGE_Table_to_Bedgraph/logFC.output.bedgraph" />
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82 <output name="fdr" file="Convert_DGE_Table_to_Bedgraph/FDR.output.bedgraph" />
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83 </test>
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84 </tests>
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85
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86 <help>
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87 P-values and FDRs are swapped from 1 to 0, and 0 to 1, because this way the most siginificant genes will obtain the highest values which is convenient for visualisation.
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88
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89 @CONTACT@
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90 </help>
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91
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92 <expand macro="citations" />
99
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93 </tool>