diff extract_variants.xml @ 0:bf8841b0a6b0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools commit a35519a8cc09ea0a6e6ac5f57ff36fd738e5adb7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_variants.xml	Mon Feb 20 06:35:42 2017 -0500
@@ -0,0 +1,79 @@
+<tool id="gvcftools_extract_variants" name="Extract Variants from gVCF files" version="0.1">
+  <description>Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file.</description>
+
+  <requirements>
+      <requirement type="package" version="0.17.0">gvcftools</requirement>
+  </requirements>
+
+  <command detect_errors="aggressive">
+  <![CDATA[
+      extract_variants
+        #if str( $advanced.advanced_options_selector ) == 'true':
+         '${advanced.skip_header}' '${advanced.invert}'
+        #end if
+      < '${gvcf_input}' > '${vcf_output}'
+  ]]>]
+  </command>
+
+  <inputs>
+    <param name="gvcf_input" type="data" format="vcf" label="Variants (gVCF format)" />
+    <conditional name="advanced">
+      <param name="advanced_options_selector" type="select" label="Advanced options">
+        <option value="true">Show advanced options</option>
+        <option value="false" selected="True">Don't show advanced options</option>
+      </param>
+      <when value="true">
+        <param type="boolean" name="skip_header" argument="--skip-header"
+          truevalue="--skip-header" falsevalue=""
+          label="Write the variants output file without a header" />
+        <param type="boolean" argument="--invert"
+          truevalue="--invert" falsevalue=""
+          label="Invert the filter so that only non-variant records are output" />
+      </when>
+      <when value="false"></when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="vcf_output" format="vcf" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
+      <output name="vcf_output" ftype="vcf" value="variants_output1.vcf" />
+    </test>
+    <test>
+      <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
+      <param name="advanced_options_selector" value="true" />
+      <param name="skip_header" value="True" />
+      <output name="vcf_output" ftype="vcf" value="variants_noheader_output1.vcf" />
+    </test>
+    <test>
+      <param name="gvcf_input" ftype="vcf" value="input1.gvcf" />
+      <param name="advanced_options_selector" value="true" />
+      <param name="invert" value="True" />
+      <output name="vcf_output" ftype="vcf" value="nonvariants_output1.vcf" />
+    </test>
+
+  </tests>
+
+  <help>
+    <![CDATA[
+    Extract variants from a gVCF field, removing all non-variant blocks to yield a smaller variant only VCF file.
+
+    From the `gvcftools`_ toolkit.
+
+    .. _gvcftools: https://sites.google.com/site/gvcftools/
+    ]]>
+  </help>
+  <citations>
+        <citation type="bibtex">
+           @unpublished{gvcftools,
+              author = {Illumina, Inc.},
+              title  = {gvcftools},
+              url    = {https://sites.google.com/site/gvcftools/}
+            }
+        </citation>
+  </citations>
+</tool>