Mercurial > repos > fcaramia > edger
comparison edgeR.xml @ 12:d49d06d35683 draft
Uploaded
| author | fcaramia |
|---|---|
| date | Wed, 21 Aug 2013 22:13:23 -0400 |
| parents | 86292c2b0ba9 |
| children |
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| 11:e5fcbabbdea7 | 12:d49d06d35683 |
|---|---|
| 1 <tool id="edgeR" name="edgeR" version="0.0.1"> | 1 <tool id="edgeR" name="edgeR" version="0.0.2"> |
| 2 <description> - Estimates differential gene expression for short read sequence count using methods appropriate for count data</description> | 2 <description> - Estimates differential gene expression for short read sequence count using methods appropriate for count data</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="R-module">edgeR</requirement> | 4 <requirement type="R-module">edgeR</requirement> |
| 5 <requirement type="R-module">limma</requirement> | 5 <requirement type="R-module">limma</requirement> |
| 6 </requirements> | 6 </requirements> |
| 8 edgeR.pl -a $analysis_type.analysis -e $html_file.files_path -f $fdr -h $html_file -o $output | 8 edgeR.pl -a $analysis_type.analysis -e $html_file.files_path -f $fdr -h $html_file -o $output |
| 9 ## Pairwise comparisons | 9 ## Pairwise comparisons |
| 10 #if $analysis_type.analysis == "pw": | 10 #if $analysis_type.analysis == "pw": |
| 11 -r $analysis_type.rowsumfilter | 11 -r $analysis_type.rowsumfilter |
| 12 #if $analysis_type.tagwise_disp.twd == "TRUE": | 12 #if $analysis_type.tagwise_disp.twd == "TRUE": |
| 13 -p $analysis_type.tagwise_disp.twd_prop | 13 -u $analysis_type.tagwise_disp.twd_trend |
| 14 -u $analysis_type.tagwise_disp.twd_trend | |
| 15 -t | 14 -t |
| 16 #end if | 15 #end if |
| 17 ## GLM | 16 ## GLM |
| 18 #else if $analysis_type.analysis == "glm": | 17 #else if $analysis_type.analysis == "glm": |
| 19 #if $analysis_type.exp.export_norm == "true": | 18 #if $analysis_type.exp.export_norm == "true": |
| 69 <param name="twd_trend" type="select" label="Method for allowing the prior distribution for the dispersion to be abundance-dependent"> | 68 <param name="twd_trend" type="select" label="Method for allowing the prior distribution for the dispersion to be abundance-dependent"> |
| 70 <option value="movingave" selected="true">Movingave</option> | 69 <option value="movingave" selected="true">Movingave</option> |
| 71 <option value="tricube">Tricube</option> | 70 <option value="tricube">Tricube</option> |
| 72 <option value="none">None</option> | 71 <option value="none">None</option> |
| 73 </param> | 72 </param> |
| 74 <param name="twd_prop" type="float" value="0.3" label="The proportion of all tags/genes to be used for the locally weighted estimation of the tagwise dispersion, allowing the dispersion estimates to vary with abundance (expression level)"/> | |
| 75 </when> | 73 </when> |
| 76 </conditional> | 74 </conditional> |
| 77 </when> | 75 </when> |
| 78 <when value="glm"> | 76 <when value="glm"> |
| 79 <param name="disp" type="select" label="Select The Dispersion Estimate To Use:"> | 77 <param name="disp" type="select" label="Select The Dispersion Estimate To Use:"> |