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annotate edgeR_Convert_DGE_Table_to_Bedgraph.xml @ 92:86c3aaa205b5 draft

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Added bedgraph exporting function for the DGE tables
author yhoogstrate
date Fri, 13 Mar 2015 05:45:09 -0400
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children 31335aa52b2e
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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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4
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5 <requirements>
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6 <requirement type="package" version="1.0.0">edger_dge_table_to_bedgraph</requirement>
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7 </requirements>
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8
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9 <command interpreter="python">
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10 edger_dge_table_to_bedgraph
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11 -t $cpm_table
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12 -g $geneset
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13
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14 #if $logfc:
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15 -c3 $logfc
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16 #end if
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17
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18 #if $logcpm:
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19 -c4 $logcpm
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20 #end if
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21
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22 #if $lr:
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23 -c5 $lr
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24 #end if
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25
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26 #if $pvalue:
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27 -c6 $pvalue
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28 #end if
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29
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30 #if $fdr:
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31 -c7 $fdr
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32 #end if
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33 </command>
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34
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35 <inputs>
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36 <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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37 <param format="gtf" name="geneset" type="data" label="Geneset used for estimating expression levels prior to expression analysis" />
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38
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39 <param name="columns" type="select" label="Desired columns" multiple="true" display="checkboxes">
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40 <option value="c3" selected="true">logFC</option>
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41 <option value="c4">logCPM</option>
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42 <option value="c5">LR</option>
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43 <option value="c6">PValue</option>
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44 <option value="c7" selected="true">FDR</option>
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45 </param>
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46 </inputs>
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47
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48 <outputs>
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49 <data fromat="bedgraph" name="logfc" label="logFC from ${cpm_table.name}">
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50 <filter>"c3" in columns</filter>
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51 </data>
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52
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53 <data fromat="bedgraph" name="logcpm" label="logCPM from ${cpm_table.name}">
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54 <filter>"c4" in columns</filter>
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55 </data>
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56
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57 <data fromat="bedgraph" name="lr" label="LR from ${cpm_table.name}">
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58 <filter>"c5" in columns</filter>
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59 </data>
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60
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61 <data fromat="bedgraph" name="pvalue" label="PValue from ${cpm_table.name}">
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62 <filter>"c6" in columns</filter>
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63 </data>
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64
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65 <data fromat="bedgraph" name="fdr" label="FDR from ${cpm_table.name}">
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66 <filter>"c7" in columns</filter>
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67 </data>
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68 </outputs>
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69
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70 <help>
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71 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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72 </help>
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73 </tool>