# HG changeset patch
# User greg
# Date 1539351992 14400
# Node ID a1e53778a82bbfb6962684f825a3437bc28d8abf
Uploaded
diff -r 000000000000 -r a1e53778a82b .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Fri Oct 12 09:46:32 2018 -0400
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+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 000000000000 -r a1e53778a82b affy2vcf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/affy2vcf.xml Fri Oct 12 09:46:32 2018 -0400
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+ genotype calls and intensities to VCF
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+ bcftools-gtc2vcf-plugin
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+ output_gender_estimate_cond['output_gender_estimate'] == "yes"
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+This tool converts Affymetrix genotype calls and intensity files to VCF format.
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+-----
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+**Required options**
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+**Other options**
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+ @misc{None,
+ journal = {None},
+ author = {Genovese, Giulio},
+ title = {None},
+ year = {None},
+ url = {https://github.com/freeseek/gtc2vcf},}
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diff -r 000000000000 -r a1e53778a82b all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample Fri Oct 12 09:46:32 2018 -0400
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+#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 000000000000 -r a1e53778a82b tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Oct 12 09:46:32 2018 -0400
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+ value, dbkey, name, path
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