# HG changeset patch
# User iuc
# Date 1474904703 14400
# Node ID 77e29e6a6101eac372856637bc9396a72c48d669
# Parent  fede8a808d3627e0e7e694fbd7da283a1632438a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f

diff -r fede8a808d36 -r 77e29e6a6101 macros.xml
--- a/macros.xml	Sat Jun 25 17:27:31 2016 -0400
+++ b/macros.xml	Mon Sep 26 11:45:03 2016 -0400
@@ -2,14 +2,14 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.40">stacks</requirement>
+            <requirement type="package" version="1.42">stacks</requirement>
             <requirement type="package" version="1.2.10">velvet</requirement>
-            <container type="docker">quay.io/mulled/stacks:1.40--1</container>
+            <container type="docker">quay.io/mulled/stacks:1.42--2</container>
             <yield/>
         </requirements>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">1.40</token>
+    <token name="@WRAPPER_VERSION@">1.42</token>
 
     <xml name="stdio">
         <stdio>
@@ -86,6 +86,10 @@
         <option value="taqI">taqI</option>
         <option value="xbaI">xbaI</option>
         <option value="xhoI">xhoI</option>
+        <option value="csp6I">csp6I</option>
+        <option value="bsaHI">bsaHI</option>
+        <option value="hpaII">hpaII</option>
+        <option value="ncoI">ncoI</option>
     </xml>
 
     <xml name="cross_types">
diff -r fede8a808d36 -r 77e29e6a6101 stacks_pstacks.xml
--- a/stacks_pstacks.xml	Sat Jun 25 17:27:31 2016 -0400
+++ b/stacks_pstacks.xml	Mon Sep 26 11:45:03 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.2">
+<tool id="stacks_pstacks" name="Stacks: pstacks" version="@WRAPPER_VERSION@.0">
     <description>find stacks from short reads mapped to a reference genome</description>
     <macros>
         <import>macros.xml</import>
@@ -80,10 +80,9 @@
 
     <outputs>
         <data format="txt" name="output_log" label="pstacks.log with ${tool.name} on ${on_string}" from_work_dir="pstacks.log" />
-
         <collection name="tabs" type="list" label="Stacks from ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.+\.tags)\.tsv$" ext="tabular" directory="stacks_outputs" />
-            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />>
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.snps)\.tsv$" ext="tabular" directory="stacks_outputs" />
             <discover_datasets pattern="(?P&lt;name&gt;.+\.alleles)\.tsv$" ext="tabular" directory="stacks_outputs" />
             <discover_datasets pattern="(?P&lt;name&gt;.+\.models)\.tsv$" ext="tabular" directory="stacks_outputs" />
         </collection>
@@ -164,4 +163,3 @@
     </help>
     <expand macro="citation" />
 </tool>
-
diff -r fede8a808d36 -r 77e29e6a6101 test-data/populations/batch_1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/populations/batch_1.vcf	Mon Sep 26 11:45:03 2016 -0400
@@ -0,0 +1,12 @@
+##fileformat=VCFv4.2
+##fileDate=20160926
+##source="Stacks v1.42"
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth">
+##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihood">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	PopA_01	PopA_02
+un	35	1_33	A	C	.	PASS	NS=2;AF=0.500	GT:DP:AD:GL	0/1:18:9,9:.,19.78,.	0/1:10:6,4:.,13.18,.
+un	90	1_88	A	C	.	PASS	NS=2;AF=0.500	GT:DP:AD:GL	0/1:18:9,9:.,19.78,.	0/1:10:4,6:.,13.18,.
diff -r fede8a808d36 -r 77e29e6a6101 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Jun 25 17:27:31 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="stacks" version="1.40">
-        <repository changeset_revision="51d4ab2c4dcf" name="package_stacks_1_40" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="velvet" version="1.2.10">
-        <repository changeset_revision="93d32326537b" name="package_velvet_1_2_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>