details: http://www.bx.psu.edu/hg/galaxy/rev/218cfbba30ce changeset: 3796:218cfbba30ce user: fubar: ross Lazarus at gmail period com date: Thu May 20 14:16:08 2010 -0400 description: Added ldindep datatype to datatypes sample Added snpwga tool sections to tool_conf.sample.main - need these
diffstat:
datatypes_conf.xml.sample | 4 ++++ tool_conf.xml.main | 28 ++++++++++++++++++++++++++++ 2 files changed, 32 insertions(+), 0 deletions(-)
diffs (57 lines):
diff -r b7cc7a53364c -r 218cfbba30ce datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Thu May 20 14:10:39 2010 -0400 +++ b/datatypes_conf.xml.sample Thu May 20 14:16:08 2010 -0400 @@ -206,6 +206,9 @@ <!-- genome graphs ucsc file - first col is always marker then numeric values to plot --> <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/> <!-- part of linkage format pedigree --> + <!-- information redundancy (LD) filtered plink pbed --> + <datatype extension="ldindep" type="galaxy.datatypes.genetics:ldIndep" display_in_upload="true"> + </datatype> <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/> <!-- linkage format pedigree (separate .map file) --> <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true"> @@ -215,6 +218,7 @@ <!-- plink compressed file - has bed extension unfortunately --> <datatype extension="pbed" type="galaxy.datatypes.genetics:Pbed" display_in_upload="true"> <converter file="pbed_to_lped_converter.xml" target_datatype="lped"/> + <converter file="pbed_ldreduced_converter.xml" target_datatype="ldindep"/> </datatype> <datatype extension="pheno" type="galaxy.datatypes.genetics:Pheno"/> <!-- phenotype file - plink format --> diff -r b7cc7a53364c -r 218cfbba30ce tool_conf.xml.main --- a/tool_conf.xml.main Thu May 20 14:10:39 2010 -0400 +++ b/tool_conf.xml.main Thu May 20 14:16:08 2010 -0400 @@ -328,4 +328,32 @@ <tool file="genetrack/genetrack_indexer.xml" /> <tool file="genetrack/genetrack_peak_prediction.xml" /> </section> + <section name="SNP/WGA: Data; Filters" id="rgdat"> + <label text="Data: Import and upload" id="rgimport" /> + <tool file="data_source/upload.xml"/> + <tool file="data_source/access_libraries.xml" /> + <tool file="data_source/hapmapmart.xml" /> + <label text="Data: Filter and Clean" id="rgfilter" /> + <tool file="rgenetics/rgClean.xml"/> + <tool file="rgenetics/rgPedSub.xml"/> + <tool file="rgenetics/rgLDIndep.xml"/> + <label text="Simulate" id="rgsim" /> + <tool file="rgenetics/rgfakePhe.xml"/> + <tool file="rgenetics/rgfakePed.xml"/> + </section> + <section name="SNP/WGA: QC; LD; Plots" id="rgqcplot"> + <label text="QC; Eigenstrat" id="rgvisual" /> + <tool file="rgenetics/rgQC.xml"/> + <tool file="rgenetics/rgEigPCA.xml"/> + <label text="LD; Manhattan/QQ; GRR" id="rgld" /> + <tool file="rgenetics/rgHaploView.xml"/> + <tool file="rgenetics/rgManQQ.xml"/> + <tool file="rgenetics/rgGRR.xml"/> + </section> + <section name="SNP/WGA: Statistical Models" id="rgmodel"> + <tool file="rgenetics/rgCaCo.xml"/> + <tool file="rgenetics/rgTDT.xml"/> + <tool file="rgenetics/rgGLM.xml"/> + <tool file="rgenetics/rgManQQ.xml"/> + </section> </toolbox>