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Changeset 8:81972652519c (2019-05-07)

Previous changeset 7:eae7c08ebb6f (2019-05-02) Next changeset 9:fa24bf0598f4 (2020-01-23)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 393a497b224cd86285052e5ca2f41edc01125503

modified:
vcffilter.xml

added:
test-data/vcffilter-test2.vcf

diff -r eae7c08ebb6f -r 81972652519c test-data/vcffilter-test2.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcffilter-test2.vcf Tue May 07 12:01:04 2019 -0400

@@ -0,0 +1,26 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##filter="!( DP > 10 )"
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
+##ALT=<ID=CNV,Description="Copy number variable region">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
+20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
+20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,.
+20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,.

diff -r eae7c08ebb6f -r 81972652519c vcffilter.xml
--- a/vcffilter.xml Thu May 02 18:33:46 2019 -0400
+++ b/vcffilter.xml Tue May 07 12:01:04 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 > 10" label="Specify filterting value" help="See explanation of filtering options below">
+            <param name="filter_value" type="text" value="DP > 10" label="Specify filtering value" help="See explanation of filtering options below">
                 <sanitizer>
                     <valid initial="string.printable">
                         <remove value="'"/>
@@ -46,6 +46,7 @@
                         <add source=""" target=""/>
                     </mapping>
                 </sanitizer>
+                <validator type="expression" message="Invalid operator provided, valid operators are =, !, <, >, |, &.">value is not None and not any(x in value for x in ["<=", "=<", ">=", "=>"])</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 > 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::