Mercurial > repos > stef > qdnaseq
changeset 36:d5ed2f8fab83 draft
Uploaded
| author | stef |
|---|---|
| date | Wed, 18 Jun 2014 08:36:28 -0400 |
| parents | 40ae44574624 |
| children | 45051afbeff4 |
| files | QDNAseq.xml |
| diffstat | 1 files changed, 9 insertions(+), 6 deletions(-) [+] |
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--- a/QDNAseq.xml Wed Jun 18 07:45:19 2014 -0400 +++ b/QDNAseq.xml Wed Jun 18 08:36:28 2014 -0400 @@ -3,23 +3,26 @@ <requirements> <!-- <requirement type="set_environment">QDNASEQ_SCRIPT_PATH</requirement> --> <!-- The R package for v3.1.0 is not ready yet --> - <!--<requirement type="package" version="3.1.0">R</requirement>--> + <!-- <requirement type="package" version="3.1.0">R</requirement>--> + <requirement type="package" version="0.1.18">samtools</requirement> <!-- <requirement type="package" version="1.0.5">bioc_qdnaseq</requirement> --> </requirements> <description>Quantitative copy number abberation detection</description> - <!-- - if case you want to use a specific R installation use the commented command block and set correct path + <!-- command block to call script with specific R installation (set full paths) --> + <!-- <command> - /ccagc/lib/R/R-3.1.0/bin/Rscript QDNAseq.R + /full/path/to/Rscript + /full/path/to/QDNAseq.R $qdnaseq_cfg </command> --> + <!-- command block to call script with default R environment --> <command interpreter="Rscript"> QDNAseq.R - $qdnaseq_cfg <!-- use a tmp config file to pass all params to R by source() --> + $qdnaseq_cfg </command> <stdio> @@ -127,7 +130,7 @@ <param name="mappability" type="integer" value="0" min="0" max="100" label="Filter bins with lower mappability" help="Will exclude all bins will lower mappability than this number (0-100)" /> - <param name="debug" type="select" label="DEBUG/TEST" help="Use inbuilt LGG data instead of input BAMs"> + <param name="debug" type="select" label="DEBUG / TEST" help="Use inbuilt LGG data instead of input BAMs"> <option value="FALSE">no</option> <option value="TRUE">yes</option> </param>