# HG changeset patch
# User devteam
# Date 1473969917 14400
# Node ID 03030ecd1961d01418519cffa2f52a6e0ced3c34
# Parent  ad12ba1db0e493a869ebf03ed85d4efb871f82b7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79

diff -r ad12ba1db0e4 -r 03030ecd1961 macros.xml
--- a/macros.xml	Mon Nov 09 12:33:58 2015 -0500
+++ b/macros.xml	Thu Sep 15 16:05:17 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 ad12ba1db0e4 -r 03030ecd1961 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 09 12:33:58 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="vcflib" version="8a5602bf07">
-        <repository changeset_revision="3ac0905f7b7c" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>
diff -r ad12ba1db0e4 -r 03030ecd1961 vcfrandomsample.xml
--- a/vcfrandomsample.xml	Mon Nov 09 12:33:58 2015 -0500
+++ b/vcfrandomsample.xml	Thu Sep 15 16:05:17 2016 -0400
@@ -1,55 +1,55 @@
-<tool id="vcfrandomsample" name="VCFrandomSample:" version="0.0.3">
-  <description>Randomly sample sites from VCF dataset</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio" />
-  <command>
-
-    #if $adv_options.adv_options_selector == True:
-        vcfrandomsample -s "${adv_options.scale_by}" -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}"
-    #else:
-        vcfrandomsample -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}" 
-    #end if                                                                      
-  </command>
-  <inputs>
-    <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/>
-    <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/>
-    <param name="random_seed" type="integer" value="17823618326" label="use this random seed" help="-p, --random-seed; use this to make results reproducible" />
-    <conditional name="adv_options">
-      <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/>
-      <when value="use_adv_controls">
-	<param name="scale_by" type="text" value="AF" label="scale sampling likelihood by this INFO field" help="-s, --scale-by; this only works for Float info fields such as AF" />
-      </when>
-      </conditional>
-  </inputs>
-  <outputs>
-    <data format="vcf" name="out_file1" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="vcf_input" value="vcflib.vcf"/>
-      <param name="rate" value="0.2" />
-      <param name="random_seed" value="1" />
-      <param name="adv_options_selector" value="False" />
-      <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" />
-    </test>
-    </tests>
-  <help>
-
-Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls).  This may be
-used to provide uniform sampling across allele frequencies, for instance (AF field in this case).
-
-Options::
-
-    -r, --rate RATE      base sampling probability per locus
-    -s, --scale-by KEY   scale sampling likelihood by this Float info field
-    -p, --random-seed N  use this random seed
-
-----
-
-Vcfrandomsample @IS_PART_OF_VCFLIB@
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcfrandomsample" name="VCFrandomSample:" version="@WRAPPER_VERSION@.0">
+    <description>Randomly sample sites from VCF dataset</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio" />
+    <command>
+        vcfrandomsample
+            #if $adv_options.adv_options_selector == "use_adv_controls":
+                -s "${adv_options.scale_by}"
+            #end if
+            -p ${random_seed}
+            -r ${rate}
+            "${vcf_input}" > "${out_file1}" 
+    </command>
+    <inputs>
+        <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/>
+        <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/>
+        <param name="random_seed" type="integer" value="17823618326" label="use this random seed"
+            help="-p, --random-seed; use this to make results reproducible" />
+        <conditional name="adv_options">
+            <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above">
+                <option value="no">Don't use advanced options</option>
+                <option value="use_adv_controls">Use advanced options</option>
+            </param>
+            <when value="" />
+            <when value="use_adv_controls">
+                <param name="scale_by" type="text" value="AF" label="scale sampling likelihood by this INFO field" help="-s, --scale-by; this only works for Float info fields such as AF" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="vcf" name="out_file1" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="vcf_input" value="vcflib.vcf"/>
+            <param name="rate" value="0.2" />
+            <param name="random_seed" value="1" />
+            <param name="adv_options_selector" value="no" />
+            <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" />
+        </test>
+    </tests>
+    <help>
+
+Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls).  This may be
+used to provide uniform sampling across allele frequencies, for instance (AF field in this case).
+
+----
+
+Vcfrandomsample @IS_PART_OF_VCFLIB@
+    </help>
+    <expand macro="citations" />
+</tool>