# HG changeset patch
# User greg
# Date 1558024715 14400
# Node ID ab822310a9ad8eaf9e9acc9f64b59fd0776f5a60
# Parent 7e1bdc122ea1e9adde1abc1e49d5df204f28ba8c
Uploaded
diff -r 7e1bdc122ea1 -r ab822310a9ad .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Thu May 16 12:38:35 2019 -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 7e1bdc122ea1 -r ab822310a9ad README
--- a/README Thu May 16 10:54:52 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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-init repo
diff -r 7e1bdc122ea1 -r ab822310a9ad affy2vcf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/affy2vcf.xml Thu May 16 12:38:35 2019 -0400
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+ genotype calls and intensities to VCF
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+ macros.xml
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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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+ * **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.
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+**Other options**
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+ * **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.
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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 7e1bdc122ea1 -r ab822310a9ad all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample Thu May 16 12:38:35 2019 -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 7e1bdc122ea1 -r ab822310a9ad macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu May 16 12:38:35 2019 -0400
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+ 1.9
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+ 10.1093/bioinformatics/btp352
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+ --threads \${GALAXY_SLOTS:-4}
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diff -r 7e1bdc122ea1 -r ab822310a9ad 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 12:38:35 2019 -0400
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+ value, dbkey, name, path
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