# HG changeset patch # User greg # Date 1558024939 14400 # Node ID b8549f504829bfc12297fb477ba937b6d7f93917 # Parent 5e9d8a4f6ac87a794cc88896a3c7de0bc9c4d913 Uploaded diff -r 5e9d8a4f6ac8 -r b8549f504829 .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Thu May 16 12:42:19 2019 -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 5e9d8a4f6ac8 -r b8549f504829 README --- a/README Thu May 16 10:59:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -init commit diff -r 5e9d8a4f6ac8 -r b8549f504829 affy2vcf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/affy2vcf.xml Thu May 16 12:42:19 2019 -0400 @@ -0,0 +1,132 @@ + + genotype calls and intensities to VCF + + macros.xml + + + bcftools-gtc2vcf-plugin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + output_gender_estimate_cond['output_gender_estimate'] == "yes" + + + + + + + + + + + + + + + + +This tool converts Affymetrix genotype calls and intensity files to VCF format. + +----- + +**Required options** + + * **Probeset annotation file** - probeset annotation file produced by the sequencing run. + * **Apt-probeset genotype summary file** - apt-probeset genotype summary file produced by the sequencing run. + * **Apt-probeset genotype snp-posteriors file** - apt-probeset genotype snp-posteriors file produced by the sequencing run. + * **Apt-probeset genotype report file** - apt-probeset genotype report file produced by the sequencing run. + * **Apt-probeset genotype confidences file** - apt-probeset genotype confidences file produced by the sequencing run. + * **Apt-probeset genotype calls file** - apt-probeset genotype calls file produced by the sequencing run. + * **Choose the source for the reference genome** - select a reference genome from your history or one installed into your local Galaxy environment by a data manager tool. + +**Other options** + + * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset. + * **Append version and command line to the header** - append version and command line to the header of the output VCF dataset. + * **Select format for output** - select one of uncompressed/compressed VCF/BCF. + + + + + @misc{None, + journal = {None}, + author = {Genovese, Giulio}, + title = {None}, + year = {None}, + url = {https://github.com/freeseek/gtc2vcf},} + + + diff -r 5e9d8a4f6ac8 -r b8549f504829 all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Thu May 16 12:42:19 2019 -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 5e9d8a4f6ac8 -r b8549f504829 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu May 16 12:42:19 2019 -0400 @@ -0,0 +1,25 @@ + + 1.9 + + 10.1093/bioinformatics/btp352 + + + + + + --threads \${GALAXY_SLOTS:-4} + + + + + + + + + + + + + diff -r 5e9d8a4f6ac8 -r b8549f504829 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu May 16 12:42:19 2019 -0400 @@ -0,0 +1,7 @@ + + + + value, dbkey, name, path + +
+