Mercurial > repos > stef > qdnaseq
comparison QDNAseq.xml @ 6:beb7abe277b3 draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 13 Jun 2014 11:01:25 -0400 |
| parents | 75d96e0555d1 |
| children | 9f4e0192de10 |
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| 5:d4747215fa6b | 6:beb7abe277b3 |
|---|---|
| 1 <tool id="QDNAseq" name="QDNAseq" version="0.0.1"> | 1 <tool id="QDNAseq" name="QDNAseq" version="0.0.1"> |
| 2 | 2 |
| 3 <requirements> | 3 <requirements> |
| 4 <!-- <requirement type="set_environment">QDNASEQ_SCRIPT_PATH</requirement> --> | 4 <requirement type="set_environment">QDNASEQ_SCRIPT_PATH</requirement> |
| 5 <requirement type="package" version="3.0.3">R</requirement> | 5 <requirement type="package" version="3.0.3">R</requirement> |
| 6 <requirement type="package" version="1.0.4">bioc_qdnaseq</requirement> | |
| 6 </requirements> | 7 </requirements> |
| 7 | 8 |
| 8 <description>Quantitative copy number abberation detection</description> | 9 <description>Quantitative copy number abberation detection</description> |
| 9 | 10 |
| 10 <command interpreter="Rscript"> | 11 <command interpreter="Rscript"> |
| 290 | 291 |
| 291 ----- | 292 ----- |
| 292 | 293 |
| 293 .. class:: warningmark | 294 .. class:: warningmark |
| 294 | 295 |
| 295 Requires internet access for downloading bin-annotations from bitbucket and to show css styling of the final report | 296 The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups. |
| 296 | 297 |
| 297 .. class:: warningmark | 298 .. class:: warningmark |
| 298 | 299 |
| 299 All R stderr is rerouted to stdout due to limitations in R. This means the tool might be marked succesful (green) while it actually isn't, closer inspection of the stdout output is required in that case. | 300 Requires **internet access** for downloading bin-annotations from bitbucket and to show css styling of the final report |
| 300 | 301 |
| 301 .. class:: warningmark | 302 .. class:: warningmark |
| 302 | 303 |
| 303 The smaller the binsize, the longer the analysis takes | |
| 304 | |
| 305 .. class:: warningmark | |
| 306 | |
| 307 If the data is noisy, a **larger binsize** should be chosen | 304 If the data is noisy, a **larger binsize** should be chosen |
| 308 | |
| 309 .. class:: warningmark | |
| 310 | |
| 311 The input BAMs are expected to be **single end reads of 50bp length** mapped to GRCh37/hg19 genome build. Other experiment setups are currently not supported within galaxy. See the documentation of QDNAseq at bioconductor on how to deal with different setups. | |
| 312 | 305 |
| 313 ----- | 306 ----- |
| 314 | 307 |
| 315 **Example** | 308 **Example** |
| 316 | 309 |