changeset 0:d4c49015dac0 draft

Uploaded

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+name: affy_ids_for_genotyping
+owner: greg
+description: |
+  Contains a tool that extracts the Affymetrix ids from a VCF file for genotyping.
+homepage_url: http://baumslab.org
+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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/affy_ids_for_genotyping.xml	Thu Aug 15 09:32:13 2019 -0400
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+<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"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_vcf" value="input.vcf" ftype="vcf"/>
+            <output name="output" file="output.tabular" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Extracts information from a VCF file that contains Affymetrix identifiers and produces a file that contains
+a subset of the identifiers combined with additional data to generate the genotype population information
+for use as input to the Corals Multilocus Genotype tool.  This tool must be able to access the corals (stag)
+database.
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{None,
+            journal = {None},
+            author = {Baums I},
+            title = {Manuscript in preparation},
+            year = {None},
+            url = {http://baumslab.org}
+        </citation>
+    </citations>
+</tool>