# HG changeset patch
# User iuc
# Date 1474904660 14400
# Node ID 998dfec32bdeb4bf76b4bb3439031bb35545196c
# Parent  bab631cc9f64178daa34e32a6eacbd499397f562
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f

diff -r bab631cc9f64 -r 998dfec32bde macros.xml
--- a/macros.xml	Sat Jun 25 17:28:47 2016 -0400
+++ b/macros.xml	Mon Sep 26 11:44:20 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 bab631cc9f64 -r 998dfec32bde stacks_denovomap.xml
--- a/stacks_denovomap.xml	Sat Jun 25 17:28:47 2016 -0400
+++ b/stacks_denovomap.xml	Mon Sep 26 11:44:20 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.1">
+<tool id="stacks_denovomap" name="Stacks: de novo map" version="@WRAPPER_VERSION@.0">
     <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description>
     <macros>
         <import>macros.xml</import>
@@ -127,8 +127,8 @@
             #end if
             -M $assembly_options.M
             -n $assembly_options.n
-            -t $assembly_options.t
-            -H $assembly_options.H
+            $assembly_options.t
+            $assembly_options.H
 
             ## Batch description
             -b 1
@@ -179,7 +179,7 @@
             <param name="P" argument="-P" type="integer" value="" optional="true" label="Minimum number of identical, raw reads required to create a stack in 'progeny' individuals" />
             <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual"/>
             <param name="N" argument="-N" type="integer" value="" optional="true" label="Number of mismatches allowed when aligning secondary reads" help="default is [-M]+2" />
-            <param name="n" argument="-n" type="integer" value="1" label="specify the number of mismatches allowed between loci when building the catalog"/>
+            <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog"/>
 
             <param name="t" argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Remove, or break up, highly repetitive RAD-Tags in the ustacks program" />
             <param name="H" argument="-H" type="boolean" checked="false" truevalue="-H" falsevalue="" label="Disable calling haplotypes from secondary reads" />
@@ -531,4 +531,3 @@
     </help>
     <expand macro="citation" />
 </tool>
-
diff -r bab631cc9f64 -r 998dfec32bde 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 11:44:20 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 bab631cc9f64 -r 998dfec32bde tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Jun 25 17:28:47 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>