Mercurial > repos > stef > qdnaseq
changeset 44:4372afee310b draft
Uploaded
| author | stef |
|---|---|
| date | Fri, 20 Jun 2014 07:14:07 -0400 |
| parents | 327b8830d49f |
| children | 945d3f371e1a |
| files | QDNAseq.xml |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/QDNAseq.xml Thu Jun 19 12:35:46 2014 -0400 +++ b/QDNAseq.xml Fri Jun 20 07:14:07 2014 -0400 @@ -48,6 +48,11 @@ <option value="1">1kb</option> </param> + <param name="doCall" type="select" label="Also segment and call with CGHcall" help="This setting will be set to yes if called output is requested (see additional history outputs)"> + <option value="TRUE">yes</option> + <option value="FALSE">no</option> + </param> + <param name="experimentType" type="select" label="Type of sequencing data" help="Currently only single end reads of lenght 50 are supported within galaxy"> <option value="SR50">Single Reads of 50bp</option> <!-- <option value="PE1000">PairedEnd1000</option> --> @@ -111,10 +116,6 @@ <option value="yes">yes</option> </param> <when value="yes"> - <param name="doCall" type="select" label="Also segment and call with CGHcall" help="This setting will be set to yes if called output is requested (see additional history outputs)"> - <option value="TRUE">yes</option> - <option value="FALSE">no</option> - </param> <param name="undo_splits" type="select" label="undoSplits" help="If set to sdundo, see undoSD below"> <option value="sdundo">sdundo</option> @@ -138,7 +139,6 @@ </when> <!-- need to set defaults because params are passed to R anyway --> <when value="no"> - <param name="doCall" type="hidden" value="TRUE" /> <param name="undoSD" type="hidden" value="1" /> <param name="undo_splits" type="hidden" value="sdundo" /> <param name="blacklist" type="hidden" value="TRUE" /> @@ -209,9 +209,9 @@ "${htmlFile}" -> outputHtml "${htmlFile.files_path}" -> outputPath "${use_own_binannotation.binannotation_file}" -> binAnnotations +as.logical( "${doCall}" ) -> doCall ## advanced options -as.logical( "${advanced.doCall}" ) -> doCall as.double( "${advanced.undoSD}" ) -> undoSD as.logical( "${advanced.debug}" ) -> debug as.logical( "${advanced.blacklist}" ) -> filterBlacklistedBins