Mercurial > repos > iuc > deseq2
comparison deseq2.xml @ 25:de44f8eff84a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 9eb6d07510ccf27d6499172d62c81661078ec57b"
| author | iuc |
|---|---|
| date | Wed, 25 Nov 2020 18:36:55 +0000 |
| parents | 71bacea10eee |
| children | 6a3a025714d3 |
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| 24:71bacea10eee | 25:de44f8eff84a |
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| 174 label="Output rLog normalized table" /> | 174 label="Output rLog normalized table" /> |
| 175 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false" | 175 <param name="normVST" type="boolean" truevalue="1" falsevalue="0" checked="false" |
| 176 label="Output VST normalized table" /> | 176 label="Output VST normalized table" /> |
| 177 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false" | 177 <param name="many_contrasts" type="boolean" truevalue="1" falsevalue="0" checked="false" |
| 178 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)" | 178 label="Output all levels vs all levels of primary factor (use when you have >2 levels for primary factor)" |
| 179 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> | 179 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> |
| 180 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors" | 180 <param name="esf" type="select" label="(Optional) Method for estimateSizeFactors" |
| 181 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq. | 181 help="Method for estimation: either 'ratio', 'poscounts', or 'iterate'. 'ratio' uses the standard median ratio method introduced in DESeq. |
| 182 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples. | 182 The size factor is the median ratio of the sample over a 'pseudosample': for each gene, the geometric mean of all samples. |
| 183 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem | 183 'poscounts' and 'iterate' offer alternative estimators, which can be used even when all genes contain a sample with a zero (a problem |
| 184 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with | 184 for the default method, as the geometric mean becomes zero, and the ratio undefined). The 'poscounts' estimator deals with a gene with |
| 201 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor | 201 counts with large Cook’s distance with the trimmed mean over all samples, scaled up by the size factor |
| 202 or normalization factor for that sample" /> | 202 or normalization factor for that sample" /> |
| 203 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" | 203 <param name="outlier_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" |
| 204 label="Turn off outliers filtering (only affects with >2 replicates)" | 204 label="Turn off outliers filtering (only affects with >2 replicates)" |
| 205 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically | 205 help="When there are more than 2 replicates for a given sample, the DESeq2 will automatically |
| 206 filter genes which contain a Cook’s distance above a cutoff" /> | 206 filter genes which contain a Cook’s distance above a cutoff" /> |
| 207 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" | 207 <param name="auto_mean_filter_off" type="boolean" truevalue="1" falsevalue="0" checked="false" |
| 208 label="Turn off independent filtering" | 208 label="Turn off independent filtering" |
| 209 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> | 209 help=" DESeq2 performs independent filtering by default using the mean of normalized counts as a filter statistic" /> |
| 210 </inputs> | 210 </inputs> |
| 211 <outputs> | 211 <outputs> |
| 212 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}"> | 212 <data name="deseq_out" format="tabular" label="DESeq2 result file on ${on_string}"> |
| 213 <filter>many_contrasts is False</filter> | 213 <filter>many_contrasts is False</filter> |
| 214 <actions> | 214 <actions> |