# HG changeset patch
# User greg
# Date 1538663677 14400
# Node ID 5f30220af0cdb8b443464884feaf807511badf3f
# Parent  4bf7233a372bce35963e24d96758d5d42fa5c88f
Uploaded

diff -r 4bf7233a372b -r 5f30220af0cd affy2vcf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/affy2vcf.xml	Thu Oct 04 10:34:37 2018 -0400
@@ -0,0 +1,84 @@
+<tool id="affr2vcf" name="Convert Affymetrix" version="1.9">
+    <description>genotype calls and intensities to VCF</description>
+    <requirements>
+        <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+#set text_outputs_dir = 'text_outputs'
+mkdir $text_outputs_dir &&
+bcftools +affy2vcf.so
+-- fasta_ref '$fasta_ref'
+--annot '$annot'
+--snp-posteriors '$text_outputs_dir/snp_posteriors.txt'
+--summary '$text_outputs_dir/summary.txt'
+--report '$text_outputs_dir/report.txt'
+--calls '$text_outputs_dir/calls.txt'
+--confidences '$text_outputs_dir/confidences.txt'
+#if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
+    --sex '$text_outputs_dir/gender_estimate.txt'
+#end if
+#if str($append_version) == "no":
+    --no-version
+#end if
+--output '$output'
+--output_type $output_type
+--threads \${GALAXY_SLOTS:-4}
+    ]]></command>
+    <inputs>
+        <param name="annot" type="data" format="csv" label="Probeset annotation file" />
+        <param name="fasta_ref" type="select" format="fasta" label="Fasta reference sequence">
+            <options from_data_table="all_fasta">
+                <column name="name" index="1"/>
+                <column name="value" index="2"/>
+                <column name="path" index="2"/>
+                <filter type="sort_by" column="1"/>
+                <validator type="no_options" message="No Fasta genome references are available.  Use the Fetch Genome DBKeys All Fasta Data Manager tool in Galaxy to install and populate the all_fasta data table."/>
+            </options>
+        </param>
+        <conditional name="output_gender_estimate_cond">
+            <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes"/>
+        </conditional>
+        <conditional name="append_version_cond">
+            <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <collection name="txt_outputs" type="list" label="${tool.name} (reports) on ${on_string}">
+            <discover_datasets pattern="__name__" directory="output" format="txt" />
+        </collection>
+        <data name="output" format="vcf" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+This tool converts Affymetrix genotype calls and intensity files to VCF format.
+
+-----
+
+**Required options**
+
+**Other options**
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @misc{None,
+            journal = {None},
+            author = {Genovese, Giulio},
+            title = {None},
+            year = {None},
+            url = {https://github.com/freeseek/gtc2vcf},}
+        </citation>
+    </citations>
+</tool>