Mercurial > repos > devteam > vcffilter

diff vcffilter.xml @ 7:7ce3b93e0883 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503
author iuc
date Tue, 07 May 2019 11:59:01 -0400
parents 447c0f9c0a9b
children af9bfb0f213e
line wrap: on
line diff
--- a/vcffilter.xml	Thu May 02 18:33:20 2019 -0400
+++ b/vcffilter.xml	Tue May 07 11:59:01 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy2">
+<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy3">
     <description>filter VCF data in a variety of attributes</description>
     <macros>
         <import>macros.xml</import>
@@ -35,7 +35,7 @@
                 <option value="-f">Info filter (-f)</option>
                 <option value="-g">Genotype filter (-g)</option>
             </param>
-            <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filterting value" help="See explanation of filtering options below">
+            <param name="filter_value" type="text" value="DP &gt; 10" label="Specify filtering value" help="See explanation of filtering options below">
                 <sanitizer>
                     <valid initial="string.printable">
                         <remove value="&apos;"/>
@@ -46,6 +46,7 @@
                         <add source="&quot;" target=""/>
                     </mapping>
                 </sanitizer>
+                <validator type="expression" message="Invalid operator provided, valid operators are =, !, &lt;, &gt;, |, &amp;.">value is not None and not any(x in value for x in ["&lt;=", "=&lt;", "&gt;=", "=&gt;"])</validator>
             </param>
         </repeat>
         <param name="filter_sites" argument="--filter-sites" type="boolean" truevalue="--filter-sites" falsevalue="" label="Filter entire records, not just alleles"/>
@@ -67,6 +68,13 @@
             <param name="input1" value="vcflib.vcf"/>
             <output name="out_file1" file="vcffilter-test1.vcf"/>
         </test>
+        <test>
+            <param name="filter_repeat_0|filter_type" value="-f"/>
+            <param name="filter_repeat_0|filter_value" value="!( DP &gt; 10 )"/>
+            <param name="invert" value="true"/>
+            <param name="input1" value="vcflib.vcf"/>
+            <output name="out_file1" file="vcffilter-test2.vcf"/>
+        </test>
     </tests>
     <help><![CDATA[
 You can specify the following options within the **Specify filtering expression** box in any combination::