--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_validate.xml	Sat Jun 01 07:20:41 2019 -0400
@@ -0,0 +1,106 @@
+<tool id="gatk2_variant_validate" name="Validate Variants" version="@VERSION@.0">
+  <description></description>
+  <macros>
+    <import>gatk2_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
+  <command interpreter="python">
+    gatk2_wrapper.py
+   --stdout "${output_log}"
+   -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
+   -p '
+   @JAR_PATH@
+    -T "ValidateVariants"
+
+    \$GATK2_SITE_OPTIONS
+
+    #if $reference_source.reference_source_selector != "history":
+        -R "${reference_source.ref_file.fields.path}"
+    #end if
+    ${warn_on_errors}
+    ${do_not_validate_filtered_records}
+   '
+    @DBSNP_OPTIONS@
+
+    #include source=$standard_gatk_options#
+  </command>
+  <inputs>
+
+    <conditional name="reference_source">
+      <expand macro="reference_source_selector_param" />
+      <when value="cached">
+        <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
+          <options from_data_table="gatk2_picard_indexes">
+            <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
+          </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+        </param>
+      </when>
+      <when value="history"> <!-- FIX ME!!!! -->
+        <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
+      </when>
+    </conditional>
+    <expand macro="dbsnp_param" />
+
+    <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/>
+    <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/>
+
+    <expand macro="gatk_param_type_conditional" />
+
+  </inputs>
+  <outputs>
+    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <tests>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
+          <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
+          <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
+          <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
+          <param name="dbsnp_rod_name" value="dbsnp" />
+          <param name="warn_on_errors" value="True"/>
+          <param name="do_not_validate_filtered_records" />
+          <param name="gatk_param_type_selector" value="basic" />
+          <output name="output_log" file="gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains" compare="contains" />
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+Validates a variants file.
+
+For more information on using the ValidateVariants module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_ValidateVariants.html&gt;`_.
+
+To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
+
+If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
+
+------
+
+**Inputs**
+
+GenomeAnalysisTK: ValidateVariants accepts variant files as input.
+
+
+**Outputs**
+
+The output is a log of variant validation.
+
+
+Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
+
+-------
+
+**Settings**::
+
+ doNotValidateFilteredRecords    should we skip validation on filtered records?
+ warnOnErrors                    should we just emit warnings on errors instead of terminating the run?
+
+@CITATION_SECTION@
+  </help>
+  <expand macro="citations" />
+</tool>