Mercurial > repos > devteam > vcffilter

changeset 5:de885f4afb7f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcffilter commit 2ceb7f04846b90fd08d440b9f40493bb0434ce26
author iuc
date Sat, 29 Dec 2018 13:57:17 -0500
parents 6b935ab36d7b
children 9442e22779ca
files vcffilter.xml
diffstat 1 files changed, 16 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/vcffilter.xml	Mon Mar 26 10:21:29 2018 -0400
+++ b/vcffilter.xml	Sat Dec 29 13:57:17 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy1">
+<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@+galaxy2">
     <description>filter VCF data in a variety of attributes</description>
     <macros>
         <import>macros.xml</import>
@@ -30,7 +30,7 @@
     ]]></command>
     <inputs>
         <param name="input1" type="data" format="vcf" label="VCF dataset to filter"/>
-        <repeat name="filter_repeat" title="Add filters">
+        <repeat name="filter_repeat" title="more filters" min="1">
             <param name="filter_type" type="select" label="Select the filter type">
                 <option value="-f">Info filter (-f)</option>
                 <option value="-g">Genotype filter (-g)</option>
@@ -39,9 +39,11 @@
                 <sanitizer>
                     <valid initial="string.printable">
                         <remove value="&apos;"/>
+                        <remove value="&quot;"/>
                     </valid>
                     <mapping initial="none">
-                        <add source="&apos;" target="__sq__"/>
+                        <add source="&apos;" target=""/>
+                        <add source="&quot;" target=""/>
                     </mapping>
                 </sanitizer>
             </param>
@@ -80,11 +82,18 @@
     -o, --or              use logical OR instead of AND to combine filters
     -r, --region          specify a region on which to target the filtering (must be used in conjunction with -f or -g)
 
-Filters are specified in the form {ID} {operator} {value}::
+To specify filters, click on the 'Insert Add filters' button, choose a filter type
+(e.g., 'Info filter' or 'Genotype filter'), and specify filter value according to the
+following pattern::
 
- -f "DP > 10"          # for info fields
- -g "GT = 1|1"         # for genotype fields
- -f "CpG"              # for 'flag' fields
+- For 'Info filter (-f)':: {ID} {operator} {value}
+    For instance::  DP > 10
+
+- For 'Genotype fields (-g)':: {ID} {operator} {value}
+    For instance::  GT = 1|1
+
+- For 'Flag' fields (when 'Info filter (-f)' is selected for filter type field):: {value}
+    For instance::  CpG
 
 Any number of filters may be specified.  They are combined via logical AND unless the --or option is specified. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields.