# HG changeset patch # User greg # Date 1538663161 14400 # Node ID 4bf7233a372bce35963e24d96758d5d42fa5c88f # Parent 197a77374215a502ec4e7007ce88e315a94ebf24 Uploaded diff -r 197a77374215 -r 4bf7233a372b .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Thu Oct 04 10:26:01 2018 -0400 @@ -0,0 +1,11 @@ +name: affy2vcf +owner: greg +description: | + Contains a tool that converts Affymetrix genotype calls and intensity files to VCF format. +homepage_url: https://github.com/freeseek/gtc2vcf +long_description: | + Contains a tool that converts Affymetrix genotype calls and intensity files to VCF format. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/convert_formats/affy2vcf +type: unrestricted +categories: + - Convert Formats diff -r 197a77374215 -r 4bf7233a372b affy2vcf.xml --- a/affy2vcf.xml Thu Oct 04 10:16:02 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,84 +0,0 @@ - - genotype calls and intensities to VCF - - bcftools-gtc2vcf-plugin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -This tool converts Affymetrix genotype calls and intensity files to VCF format. - ------ - -**Required options** - -**Other options** - - - - @misc{None, - journal = {None}, - author = {Genovese, Giulio}, - title = {None}, - year = {None}, - url = {https://github.com/freeseek/gtc2vcf},} - - - diff -r 197a77374215 -r 4bf7233a372b all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Thu Oct 04 10:26:01 2018 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +# +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# diff -r 197a77374215 -r 4bf7233a372b tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Oct 04 10:26:01 2018 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+