# HG changeset patch
# User greg
# Date 1543951210 18000
# Node ID b37deda778b9333eddcede48ab7dc2ad8b86b2ab

Uploaded

diff -r 000000000000 -r b37deda778b9 .shed.yml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml	Tue Dec 04 14:20:10 2018 -0500
@@ -0,0 +1,11 @@
+name: affy_ids_for_genotyping
+owner: greg
+description: |
+  Contains a tool that extracts the Affymetrix ids from a VCF file for genotyping.
+homepage_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/corals/affy_ids_for_genotyping
+long_description: |
+  Contains a tool that extracts the Affymetrix ids from a VCF file for genotyping.
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/corals/affy_ids_for_genotyping
+type: unrestricted
+categories:
+  - Micro-array Analysis
diff -r 000000000000 -r b37deda778b9 affy_ids_for_genotyping.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/affy_ids_for_genotyping.xml	Tue Dec 04 14:20:10 2018 -0500
@@ -0,0 +1,32 @@
+<tool id="affy_ids_for_genotyping" name="Extract Affymetrix ids for genotyping" version="1.0.0">
+    <description>from VCF data</description>
+    <command detect_errors="exit_code"><![CDATA[
+grep "#CHROM" '$input_vcf' > test.head
+tr '\t' '\n' < test.head > samples.txt
+sed -i 1,9d samples.txt
+awk -F'\t' -v OFS='\t' 'NR==0 {print ; next}{print (NR),$0}' samples.txt > '$output'
+]]></command>
+    <inputs>
+        <param name="input_vcf" type="data" format="vcf" label="VCF file"/>
+        <param name="input_sample_names" type="data" format="txt" label="Sample attributes file"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_vcf" value="input.vcf" ftype="vcf"/>
+            <param name="input_sample_names" value="input_sample_names.txt" ftype="txt"/>
+            <output name="output" file="output.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Generates a file that contains the Affymetrix identifiers that will be combined with additional data to
+generate the genotype populatiuon information for use as input to the multilocus_genotype tool.  This tool
+can be used only within a Galaxy instance that includes the complementary corals (stag) database.
+    </help>
+    <citations>
+    </citations>
+</tool>