# HG changeset patch
# User iuc
# Date 1474904747 14400
# Node ID ff04b37486543054349375fbd219b321e02865d5
# Parent  216c469422d2ac211f62de261f45e050f622ff20
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f

diff -r 216c469422d2 -r ff04b3748654 macros.xml
--- a/macros.xml	Sat Jun 25 17:28:03 2016 -0400
+++ b/macros.xml	Mon Sep 26 11:45:47 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 216c469422d2 -r ff04b3748654 stacks_ustacks.xml
--- a/stacks_ustacks.xml	Sat Jun 25 17:28:03 2016 -0400
+++ b/stacks_ustacks.xml	Mon Sep 26 11:45:47 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.1">
+<tool id="stacks_ustacks" name="Stacks: ustacks" version="@WRAPPER_VERSION@.0">
     <description>align short reads into stacks</description>
     <macros>
         <import>macros.xml</import>
@@ -38,7 +38,7 @@
             -t $inputype
 
             ## Batch description
-            -i $sample_id
+            -i 1
 
             -m $m
             -M $M
@@ -81,8 +81,6 @@
     <inputs>
         <param name="sample" argument="-f" format="fastqsanger,fasta" type="data" label="Input short reads from an individual" />
 
-        <param name="sample_id" argument="-i" type="integer" value="" label="Give a unique numeric ID to this sample"/>
-
         <param name="m" argument="-m" type="integer" value="2" label="Minimum depth of coverage required to create a stack"/>
         <param name="M" argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
         <param name="R" argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads" />
@@ -115,7 +113,7 @@
 
         <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>
@@ -124,7 +122,6 @@
     <tests>
         <test>
             <param name="sample" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />
-            <param name="sample_id" value="4" />
 
             <output name="output_log">
                 <assert_contents>
@@ -196,4 +193,3 @@
     </help>
     <expand macro="citation" />
 </tool>
-
diff -r 216c469422d2 -r ff04b3748654 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 11:45:47 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 216c469422d2 -r ff04b3748654 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Jun 25 17:28:03 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>