Mercurial > repos > iuc > goseq
comparison goseq.xml @ 4:ae39895af5fe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0798278a90c08228a386516881680b328fc33f0c
| author | iuc |
|---|---|
| date | Sun, 30 Sep 2018 09:27:05 -0400 |
| parents | 783e8b70b047 |
| children | bbcf5f7f2af2 |
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| 3:783e8b70b047 | 4:ae39895af5fe |
|---|---|
| 1 <tool id="goseq" name="goseq" version="1.30.0"> | 1 <tool id="goseq" name="goseq" version="1.30.1"> |
| 2 <description>tests for overrepresented gene categories</description> | 2 <description>tests for overrepresented gene categories</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.6.0">r-optparse</requirement> | 4 <requirement type="package" version="1.6.0">r-optparse</requirement> |
| 5 <requirement type="package" version="1.30.0">bioconductor-goseq</requirement> | 5 <requirement type="package" version="1.30.0">bioconductor-goseq</requirement> |
| 6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> | 6 <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> |
| 311 ----- | 311 ----- |
| 312 | 312 |
| 313 **Outputs** | 313 **Outputs** |
| 314 | 314 |
| 315 * This tool outputs a tabular file containing a ranked list of gene categories, similar to below. The default output is the Wallenius method table. If the Sampling and/or Hypergeometric methods are also selected, additional tables are produced. | 315 * This tool outputs a tabular file containing a ranked list of gene categories, similar to below. The default output is the Wallenius method table. If the Sampling and/or Hypergeometric methods are also selected, additional tables are produced. |
| 316 * Optionally, this tool can also output a plot of the top 10 over-represented categories, some diagnostic plots and an RData file, see **Output Options** above. | 316 * Optionally, this tool can also output a plot of the top 10 over-represented GO categories, some diagnostic plots and an RData file, see **Output Options** above. |
| 317 | 317 |
| 318 Example: | 318 Example: |
| 319 | 319 |
| 320 =========== =============== ================ ============ ========== ======================================== ========== =================== ==================== | 320 =========== =============== ================ ============ ========== ======================================== ========== =================== ==================== |
| 321 *category* *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term* *ontology* *p.adjust.over_rep* *p.adjust.under_rep* | 321 *category* *over_rep_pval* *under_rep_pval* *numDEInCat* *numInCat* *term* *ontology* *p.adjust.over_rep* *p.adjust.under_rep* |