Mercurial > repos > geert-vandeweyer > dc_genotyper
changeset 4:92207f2ec144 draft
Various Fixes and added tool_data_conf
| author | geert-vandeweyer |
|---|---|
| date | Thu, 25 Sep 2014 06:01:11 -0400 |
| parents | 61b6d523acd9 |
| children | 5c72a91ce518 |
| files | DC_Genotyper.xml DC_Genotyper_indexes.loc.sample DC_Genotyper_indexes.log.sample readme.rst tool_data_table_conf.xml.sample |
| diffstat | 5 files changed, 40 insertions(+), 46 deletions(-) [+] |
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--- a/DC_Genotyper.xml Thu Sep 25 05:36:54 2014 -0400 +++ b/DC_Genotyper.xml Thu Sep 25 06:01:11 2014 -0400 @@ -52,7 +52,6 @@ <when value="history"> <param name="ownFile" type="data" format="vcf,bcf" label="Select a dbSNP file from history"/> </when> - </param> </conditional> <param name="mincov" value="400" type="integer" label="Minimal Coverage Depth" /> <param name="ploidy" type="integer" value='10' label="Expected Sample Ploidy" /> @@ -60,7 +59,7 @@ <outputs> <data format='txt' name="output1" label="${tool.name} on ${on_string}: Allele Fraction Distributions"/> - <data format='vcf' name='output2' label="${tool.name} on ${on_string}: VCF file"> + <data format='vcf' name='output2' label="${tool.name} on ${on_string}: VCF file" /> </outputs> <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/DC_Genotyper_indexes.loc.sample Thu Sep 25 06:01:11 2014 -0400 @@ -0,0 +1,26 @@ +#This is a sample file distributed with Galaxy that enables the DC_Genotyper +#tool to locate genome files for use with twoBitToFa, and IGVtools. You will +#need to supply these files and then create a DC_Genotyper.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The DC_Genotyper.loc +#file has this format (white space characters are TAB characters): +# +#<unique_build_id> <display_name> <2bit_path;IGVtools_genome.path> +# +#for example: +# +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit;/depot/data2/galaxy/igvtools/hg19.chrom.sizes +# +#then your /depot/data2/galaxy/twobit/ directory +#would need to contain the following 2bit files: +# +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit +# +# your igvtools folder needs the following files: +# +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.chrom.sizes +# +# igv chrom.sizes files are tab delimited files. First column is chromosome name, second column is length. Additional columns are ignored. +# example genome files are included in the installation location of the package_igvtools repository. +
--- a/DC_Genotyper_indexes.log.sample Thu Sep 25 05:36:54 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,26 +0,0 @@ -#This is a sample file distributed with Galaxy that enables the DC_Genotyper -#tool to locate genome files for use with twoBitToFa, and IGVtools. You will -#need to supply these files and then create a DC_Genotyper.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The DC_Genotyper.loc -#file has this format (white space characters are TAB characters): -# -#<unique_build_id> <display_name> <2bit_path;IGVtools_genome.path> -# -#for example: -# -#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit;/depot/data2/galaxy/igvtools/hg19.chrom.sizes -# -#then your /depot/data2/galaxy/twobit/ directory -#would need to contain the following 2bit files: -# -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit -# -# your igvtools folder needs the following files: -# -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.chrom.sizes -# -# igv chrom.sizes files are tab delimited files. First column is chromosome name, second column is length. Additional columns are ignored. -# example genome files are included in the installation location of the package_igvtools repository. -
--- a/readme.rst Thu Sep 25 05:36:54 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -BACKGROUND: - -DC_Genotyper stands for Deep-Coverage Genotyper, and is aimed at detecting low fraction SNPs (no indels) in high-ploidy (or pooled) samples with very high coverage. It is being developed at the University of Antwerp by Geert Vandeweyer. - -METHOD: - -DC_Genotyper generates a background noise distributions on a per-sample basis, and uses these distrubutions to detect non-reference sites. For non-reference sites, Allele-specific distributions are used to estimate if an allele surpasses the background signal (e.g. A_to_G has different distribution as A_to_C, also reflected in Tr/Tv ratios). - -LIMITATION: - -This is a very early version with several limitations. Current limitations are : no support for indels, no plotting of the noise-models, incorrect syntax in for multi-allelic sites in the VCF file. - -Any feedback is welcome - - -INSTALLATION: - -After installation, complete the dbsnp.loc and dc_genotyper_indexes.loc files. DCG supports multithreading, but keep tests have shown that using more than 6-8 threads will lead to I/O bottlenecks.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Sep 25 06:01:11 2014 -0400 @@ -0,0 +1,13 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all index files under genome directory --> + <table name="DC_Genotyper_indexes" comment_char="#"> + <columns>name,value, path</columns> + <file path="DC_Genotyper_indexes.loc" /> + </table> + <table name="dbsnp_indexes" comment_char="#"> + <columns>name,value, path</columns> + <file path="dbsnp_indexes.loc" /> + </table> + +</tables>