# 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
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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 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
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- genotype calls and intensities to VCF
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- bcftools-gtc2vcf-plugin
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-This tool converts Affymetrix genotype calls and intensity files to VCF format.
-
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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 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
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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 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
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+ value, dbkey, name, path
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