# HG changeset patch
# User devteam
# Date 1473969948 14400
# Node ID 2d3c06c7e1f92af4620d192614b73fa991244d30
# Parent  e729e584cd6fb1653c37c602f2d626eb83ebf23b
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79

diff -r e729e584cd6f -r 2d3c06c7e1f9 macros.xml
--- a/macros.xml	Wed Nov 11 12:59:23 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:05:48 2016 -0400
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="8a5602bf07">vcflib</requirement>
+            <requirement type="package" version="1.0.0_rc1">vcflib</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -10,6 +10,7 @@
             <exit_code range="1:" level="fatal" />
         </stdio>
     </xml>
+   <token name="@WRAPPER_VERSION@">1.0.0_rc1</token>
    	<xml name="citations">
    	     <citations>
              <citation type="bibtex">
diff -r e729e584cd6f -r 2d3c06c7e1f9 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:59:23 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="vcflib" version="8a5602bf07">
-        <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="tabix" version="0.2.6">
-        <repository changeset_revision="389d2376b60b" name="package_tabix_0_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
diff -r e729e584cd6f -r 2d3c06c7e1f9 vcffilter.xml
--- a/vcffilter.xml	Wed Nov 11 12:59:23 2015 -0500
+++ b/vcffilter.xml	Thu Sep 15 16:05:48 2016 -0400
@@ -1,78 +1,77 @@
-<tool id="vcffilter2" name="VCFfilter:" version="0.0.3">
-  <description>filter VCF data in a variety of attributes</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements">
-    <requirement type="package" version="0.2.6">tabix</requirement>
-  </expand>
-  <expand macro="stdio" />
-  <command>
-  <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg -->
-    ln -s "${input1}" input1.vcf &amp;&amp;
-    bgzip input1.vcf &amp;&amp;
-    tabix -p vcf input1.vcf.gz &amp;&amp;
-    vcffilter ${filterList} input1.vcf.gz  > "${out_file1}"
-  </command>
-  
-  <inputs>
-    <param name="filterList" type="text" value="-f &quot;DP &gt; 10&quot;" label="Specify filterting expression" help="See explanation of filtering options below">
-      <sanitizer>
-        <valid initial="string.printable">
-	  <remove value="&apos;"/>
-        </valid>
-        <mapping initial="none">
-          <add source="&apos;" target="__sq__"/>
-        </mapping>
-      </sanitizer>
-    </param>
-    <param format="vcf" name="input1" type="data" label="VCF dataset to filter">
-    </param>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
- <tests>
-    <test>
-      <param name="filterList" value="-f &quot;DP &gt; 10&quot;"/>
-      <param name="input1" value="vcflib.vcf"/>
-      <output name="out_file1" file="vcffilter-test1.vcf"/>
-    </test>
-</tests> 
- <help>
-
-You can specify the following options within the **Specify filtering expression** box in any combination::
-
-    -f, --info-filter     specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
-    -g, --genotype-filter specifies a filter to apply to the genotype fields of records
-    -s, --filter-sites    filter entire records, not just alleles
-    -t, --tag-pass        tag vcf records as positively filtered with this tag, print all records
-    -F, --tag-fail        tag vcf records as negatively filtered with this tag, print all records
-    -A, --append-filter   append the existing filter tag, don't just replace it
-    -a, --allele-tag      apply -t on a per-allele basis.  adds or sets the corresponding INFO field tag
-    -v, --invert          inverts the filter, e.g. grep -v
-    -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}::
-
- -f "DP > 10"          # for info fields
- -g "GT = 1|1"         # for genotype fields
- -f "CpG"              # for 'flag' fields
-
-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.  
-
-Operators can be any of: =, !, &lt;, &gt;, pipe, &amp;
-
-
-To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f)::
-
- -r chr20:14000-15000  # only output calls between positions 14,000 and 15,000 on chromosome 20
- -r chrX               # only output call on chromosome X
-
------
-
-Vcffilter @IS_PART_OF_VCFLIB@
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcffilter2" name="VCFfilter:" version="@WRAPPER_VERSION@.0">
+    <description>filter VCF data in a variety of attributes</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="1.3">htslib</requirement>
+        <requirement type="package" version="0.2.6">tabix</requirement>
+    </expand>
+    <expand macro="stdio" />
+    <command>
+        <!-- This tools depends on tabix functionality, which is currently distributed with Galaxy itself via a pysam egg -->
+        ln -s "${input1}" input1.vcf &amp;&amp;
+        bgzip input1.vcf &amp;&amp;
+        tabix -p vcf input1.vcf.gz &amp;&amp;
+        vcffilter ${filterList} input1.vcf.gz  > "${out_file1}"
+    </command>
+
+    <inputs>
+        <param name="filterList" type="text" value="-f &quot;DP &gt; 10&quot;" label="Specify filterting expression" help="See explanation of filtering options below">
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+                <mapping initial="none">
+                    <add source="&apos;" target="__sq__"/>
+                </mapping>
+            </sanitizer>
+        </param>
+        <param format="vcf" name="input1" type="data" label="VCF dataset to filter"/>
+    </inputs>
+    <outputs>
+        <data format="vcf" name="out_file1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="filterList" value="-f &quot;DP &gt; 10&quot;"/>
+            <param name="input1" value="vcflib.vcf"/>
+            <output name="out_file1" file="vcffilter-test1.vcf"/>
+        </test>
+    </tests>
+    <help>
+You can specify the following options within the **Specify filtering expression** box in any combination::
+
+    -f, --info-filter     specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
+    -g, --genotype-filter specifies a filter to apply to the genotype fields of records
+    -s, --filter-sites    filter entire records, not just alleles
+    -t, --tag-pass        tag vcf records as positively filtered with this tag, print all records
+    -F, --tag-fail        tag vcf records as negatively filtered with this tag, print all records
+    -A, --append-filter   append the existing filter tag, don't just replace it
+    -a, --allele-tag      apply -t on a per-allele basis.  adds or sets the corresponding INFO field tag
+    -v, --invert          inverts the filter, e.g. grep -v
+    -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}::
+
+ -f "DP > 10"          # for info fields
+ -g "GT = 1|1"         # for genotype fields
+ -f "CpG"              # for 'flag' fields
+
+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.
+
+Operators can be any of: =, !, &lt;, &gt;, pipe, &amp;
+
+
+To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f)::
+
+ -r chr20:14000-15000  # only output calls between positions 14,000 and 15,000 on chromosome 20
+ -r chrX               # only output call on chromosome X
+
+-----
+
+Vcffilter @IS_PART_OF_VCFLIB@
+    </help>
+    <expand macro="citations" />
+</tool>