Mercurial > repos > iuc > snpsift

diff snpSift_rmInfo.xml @ 13:ed810da439cc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
author iuc
date Tue, 07 Jun 2016 09:41:13 -0400
parents b884686a80dc
children 80da7fae14b8
line wrap: on
line diff
--- a/snpSift_rmInfo.xml	Tue Oct 13 17:31:24 2015 -0400
+++ b/snpSift_rmInfo.xml	Tue Jun 07 09:41:13 2016 -0400
@@ -1,12 +1,14 @@
-<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="4.0.0">
+<tool id="snpSift_rmInfo" name="SnpSift rmInfo" version="@WRAPPER_VERSION@.0">
     <description>remove INFO field annotations</description>
     <macros>
         <import>snpSift_macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-      java -Xmx2G -jar \$SNPEFF_JAR_PATH/SnpSift.jar rmInfo $input ' '.join($info_fields.split(',')) > $output
+    <expand macro="version_command" />
+    <command><![CDATA[
+      java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" rmInfo "$input" ' '.join($info_fields.split(',')) > "$output"
+]]>
     </command>
     <inputs>
         <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
@@ -39,18 +41,18 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 This command removes INFO fields from a VCF file (i.e. removes annotations)
 
-Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later.
+Removing INFO fields is usually done because you want to re-annotate the VCF file, thus removing old INFO fields in order to add new ones later. 
 
-SnpEff &amp; SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate.
-The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry  in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones.
+SnpEff & SnpSift only add annotations and do not change current ones. So, in order to re-annotate a file, you should first remove the old annotations and then re-annotate. 
+The reason for this behavior is simply because replacing annotation values is considered a bad practice. Imagine that you have a VCF entry  in your re-annotated file having the value "AA=1": How do you know if this is from the old annotations or from the new ones? This confusion often leads to problems in downstream steps of your pipelines, so it's better to avoid the problem by first removing all the previous annotations and then adding the new ones. 
 
 @EXTERNAL_DOCUMENTATION@
     http://snpeff.sourceforge.net/SnpSift.html#rmInfo
 
-@CITATION_SECTION@
-
+]]>
     </help>
+    <expand macro="citations" />
 </tool>