Mercurial > repos > elixir-it > covacs_tabix

changeset 0:a408f7737cf0 draft default tip

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author elixir-it
date Thu, 08 Nov 2018 12:57:58 -0500
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files covacs_tabix.xml
diffstat 1 files changed, 38 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/covacs_tabix.xml	Thu Nov 08 12:57:58 2018 -0500
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+ <tool id="covacs_tabix" name="covacs_tabix" version="0.2.6">
+  <description> tabix wrapper for covacs </description>
+  <macros>
+  </macros>
+  <requirements>
+  	<requirement type="package" version="0.2.6" >tabix</requirement>
+  </requirements>
+  <command>
+    <![CDATA[
+	
+        ln -s $input1 covacs.vcf &&
+
+	bgzip covacs.vcf &&
+	tabix covacs.vcf.gz           
+
+	]]>
+  </command>
+  <inputs>
+    <param format="vcf" name="input1" label="input vcf " type="data" optional="true" />
+  </inputs>
+  <outputs>
+    <data format="bgzip" name="bgzip_output" from_work_dir="covacs.vcf.gz" label="bgzip on ${on_string}"/>
+    <data format="tabix" name="tabix_output" from_work_dir="covacs.vcf.gz.tbi" label="tabix on ${on_string}"/>
+  </outputs>
+  <help>
+The final output of the wrapper  consists of two files
+
+- file.vcf.gz from bgzip
+- file.vcf.gz.tbi from tabix
+
+**more informations** at http://www.htslib.org/doc/tabix.html
+  </help>
+  <citations>
+        <citation type="doi">10.1186/s12864-018-4508-1</citation>
+        <citation type="doi">10.1093/bioinformatics/btq671</citation>
+  </citations>
+</tool>
+