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1 <tool id="rgDGE" name="Digital differential expression" version="0.01">
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2 <description>for RNA counts</description>
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3 <command interpreter="python">rgDGE.py --output_html "$html_file.files_path" --input_matrix "$input1" --treatcols "$Treat_cols"
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4 --treatname "$treatment_name" --ctrlcols "$Control_cols" --ctrlname "$control_name" --output_tab "$outtab" --output_html
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5 "$html_file" --output_dir "$html_file.files_path" --method "edgeR"
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6 </command>
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7 <inputs>
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8 <param name="input1" type="data" format="tabular" label="Select an input matrix - rows are contigs, columns are counts for each sample"
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9 help="Use the DGE matrix preparation tool to create these matrices from BAM files and a BED file of contigs"/>
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10 <param name="treatment_name" type="text" value="Treatment" size="50" label="Treatment Name"/>
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11 <param name="Treat_cols" label="Select columns containing treatment." type="data_column" data_ref="input1" numerical="True"
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12 multiple="true" use_header_names="true" size="120" display="checkboxes">
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13 <validator type="no_options" message="Please select at least one column."/>
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14 </param>
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15
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16 <param name="control_name" type="text" value="Control" size="50" label="Control Name"/>
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17 <param name="Control_cols" label="Select columns containing control." type="data_column" data_ref="input1" numerical="True"
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18 multiple="true" use_header_names="true" size="120" display="checkboxes">
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19 <validator type="no_options" message="Please select at least one column."/>
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20 </param>
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21
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22 <param name="method" type="select" label="Method" >
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23 <option value="edgeR" selected="true">edgeR</option>
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24 <option value="DESeq">DESeq - coming soonish!</option>
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25 </param>
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26
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27 </inputs>
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28 <outputs>
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29 <data format="tabular" name="outtab" label="${on_string}_DGE.xls"/>
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30 <data format="html" name="html_file" label="${on_string}_DGE.html"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name='input1' value='DGEtest.xls' ftype='tabular' />
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35 <param name='treatment_name' value='case' />
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36 <param name='control_name' value='control' />
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37 <param name='Treat_cols' value='c3,c6,c9' />
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38 <param name='Control_cols' value='c2,c5,c8' />
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39 <output name='outtab' file='DGEtest1out.xls' ftype='tabular' compare='diff' />
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40 <output name='html_file' file='DGEtest1out.html' ftype='html' compare='diff' lines_diff='20' />
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41 </test>
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42 </tests>
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43 <help>
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44 .. class:: infomark
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45
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46 **What it does**
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47
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48 Performs digital differential gene expression analysis between two groups (eg a treatment and control) each with biological replicates, from count data arranged in a matrix as a tabular file.
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49
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50 **Input**
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51
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52 A matrix consisting of non-negative integers. The matrix must have a unique header row identifiying the samples, as well as a unique set of row names
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53 as the first column. To create appropriate input files, the "Multiple BAMs to matrix" tool takes multiple bam files containing mapped RNAseq reads mapped to a reference genome, and a BED file containing (eg Refseq) contigs. A count matrix containing contigs as rows and samples as
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54 columns will be created and can then be used in this tool to estimate differential gene expression using methods appropriate for count data.
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55
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56 **Output**
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57
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58 A tabular file containing relative expression levels, statistical estimates of differential expression probability, the R script, log and sessionInfo, and some helpful diagnostic plots.
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59
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60 .. class:: infomark
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61
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62 **Attribution**
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63 DGE.R was originally written by: S.Lunke and A.Kaspi.
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64 Wrapping for Galaxy and general kibbitzing from Ross Lazarus.
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65 This tool wrapts the edgeR_ Bioconductor package so all calculations and plots are controlled by that code. See edgeR_ for all documentation and appropriate attribution.
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66 Recommended reference is Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth, PMCID: PMC2796818
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67
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68 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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69 .. _edgeR: http://www.bioconductor.org/packages/2.3/bioc/html/edgeR.html
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70
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71 </help>
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72
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73 </tool>
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74
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75
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