# HG changeset patch
# User devteam
# Date 1446561405 18000
# Node ID d8c9597bfb097023e09827f2bdf7f5786f87a092
# Parent  09a7281d24c596fa4f8f5b4f711e2e91741e6729
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd

diff -r 09a7281d24c5 -r d8c9597bfb09 bwa-mem.xml
--- a/bwa-mem.xml	Tue Jul 21 14:12:49 2015 -0400
+++ b/bwa-mem.xml	Tue Nov 03 09:36:45 2015 -0500
@@ -1,14 +1,11 @@
 <?xml version="1.0"?>
-<tool id="bwa_mem" name="Map with BWA-MEM" version="0.3.1">
+<tool id="bwa_mem" name="Map with BWA-MEM" version="0.4.1">
   <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
   <macros>
     <import>read_group_macros.xml</import>
     <import>bwa_macros.xml</import>
   </macros>
-  <requirements>
-    <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
-    <requirement type="package" version="1.1">samtools</requirement>
-  </requirements>
+  <expand macro="requirements" />
   <expand macro="stdio" />
   <command>
     #set $reference_fasta_filename = "localref.fa"
@@ -170,7 +167,7 @@
       <when value="paired">
         <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
         <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
-        <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
+        <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
           <sanitizer invalid_char="">
             <valid initial="string.digits"><add value=","/> </valid>
           </sanitizer>
@@ -181,7 +178,7 @@
       </when>
       <when value="paired_collection">
         <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
-        <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
+        <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
           <sanitizer invalid_char="">
             <valid initial="string.digits"><add value=","/> </valid>
           </sanitizer>
@@ -189,7 +186,7 @@
       </when>
       <when value="paired_iv">
         <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
-        <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
+        <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
           <sanitizer invalid_char="">
             <valid initial="string.digits"><add value=","/> </valid>
           </sanitizer>
diff -r 09a7281d24c5 -r d8c9597bfb09 bwa.xml
--- a/bwa.xml	Tue Jul 21 14:12:49 2015 -0400
+++ b/bwa.xml	Tue Nov 03 09:36:45 2015 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="bwa" name="Map with BWA" version="0.3.1">
+<tool id="bwa" name="Map with BWA" version="0.4.1">
   <description>- map short reads (&lt; 100 bp) against reference genome</description>
   <macros>
     <import>read_group_macros.xml</import>
@@ -65,11 +65,7 @@
       </when>
     </xml>
   </macros>
-
-  <requirements>
-    <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
-    <requirement type="package" version="1.1">samtools</requirement>
-  </requirements>
+  <expand macro="requirements" />
   <expand macro="stdio" />
   <command>
     #set $reference_fasta_filename = "localref.fa"
diff -r 09a7281d24c5 -r d8c9597bfb09 bwa_macros.xml
--- a/bwa_macros.xml	Tue Jul 21 14:12:49 2015 -0400
+++ b/bwa_macros.xml	Tue Nov 03 09:36:45 2015 -0500
@@ -1,20 +1,27 @@
 <macros>
   <import>read_group_macros.xml</import>
   <token name="@set_rg_string@">
-      #set $rg_string = "@RG\tID:" + str($rg_id)
-      #set $rg_string += $format_read_group("\tSM:", $rg_sm)
-      #set $rg_string += $format_read_group("\tPL:", $rg_pl)
-      #set $rg_string += $format_read_group("\tLB:", $rg_lb)
-      #set $rg_string += $format_read_group("\tCN:", $rg_cn)
-      #set $rg_string += $format_read_group("\tDS:", $rg_ds)
-      #set $rg_string += $format_read_group("\tDT:", $rg_dt)
-      #set $rg_string += $format_read_group("\tFO:", $rg_fo)
-      #set $rg_string += $format_read_group("\tKS:", $rg_ks)
-      #set $rg_string += $format_read_group("\tPG:", $rg_pg)
-      #set $rg_string += $format_read_group("\tPI:", $rg_pi)
-      #set $rg_string += $format_read_group("\tPU:", $rg_pu)
+      #set $rg_string = "@RG\\tID:" + str($rg_id)
+      #set $rg_string += $format_read_group("\\tSM:", $rg_sm)
+      #set $rg_string += $format_read_group("\\tPL:", $rg_pl)
+      #set $rg_string += $format_read_group("\\tLB:", $rg_lb)
+      #set $rg_string += $format_read_group("\\tCN:", $rg_cn)
+      #set $rg_string += $format_read_group("\\tDS:", $rg_ds)
+      #set $rg_string += $format_read_group("\\tDT:", $rg_dt)
+      #set $rg_string += $format_read_group("\\tFO:", $rg_fo)
+      #set $rg_string += $format_read_group("\\tKS:", $rg_ks)
+      #set $rg_string += $format_read_group("\\tPG:", $rg_pg)
+      #set $rg_string += $format_read_group("\\tPI:", $rg_pi)
+      #set $rg_string += $format_read_group("\\tPU:", $rg_pu)
   </token>
 
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
+      <requirement type="package" version="1.2">samtools</requirement>
+    </requirements>
+  </xml>
+
   <xml name="stdio">
       <stdio>
           <exit_code range="1:" />
diff -r 09a7281d24c5 -r d8c9597bfb09 read_group_macros.xml
--- a/read_group_macros.xml	Tue Jul 21 14:12:49 2015 -0400
+++ b/read_group_macros.xml	Tue Nov 03 09:36:45 2015 -0500
@@ -146,7 +146,7 @@
         </when>
     </xml>
     <xml name="read_group_id_param">
-        <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
+        <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
             <validator type="empty_field" />
         </param>
     </xml>
@@ -158,7 +158,7 @@
         </conditional>
     </xml>
     <xml name="read_group_sm_param">
-        <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
+        <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
     </xml>
     <xml name="read_group_sm_conditional">
         <conditional name="read_group_sm_conditional">
@@ -171,7 +171,7 @@
          as per Picard.
     -->
     <xml name="read_group_sm_param_required">
-        <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
+        <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
             <validator type="empty_field" />
         </param>
     </xml>
@@ -194,7 +194,7 @@
         </param>
     </xml>
     <xml name="read_group_lb_param">
-        <param name="LB" type="text" size="25" label="Library name (LB)" optional="true" />
+        <param name="LB" type="text" label="Library name (LB)" optional="true" />
     </xml>
     <xml name="read_group_lb_conditional">
         <conditional name="read_group_lb_conditional">
@@ -204,7 +204,7 @@
         </conditional>
     </xml>
     <xml name="read_group_lb_required_param">
-        <param name="LB" type="text" size="25" label="Library name (LB)" optional="false">
+        <param name="LB" type="text" label="Library name (LB)" optional="false">
             <validator type="empty_field" />
         </param>
     </xml>
@@ -216,33 +216,33 @@
         </conditional>
     </xml>
     <xml name="read_group_cn_param">
-        <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" />
+        <param name="CN" type="text" label="Sequencing center that produced the read (CN)" />
     </xml>
     <xml name="read_group_ds_param">
-        <param name="DS" type="text" size="25" label="Description (DS)" />
+        <param name="DS" type="text" label="Description (DS)" />
     </xml>
     <xml name="read_group_dt_param">
-        <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
+        <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
     </xml>
     <xml name="read_group_fo_param">
-        <param name="FO" type="text" size="25" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
+        <param name="FO" type="text" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
           <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
         </param>
     </xml>
     <xml name="read_group_ks_param">
-        <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
+        <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
     </xml>
     <xml name="read_group_pg_param">
-        <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" />
+        <param name="PG" type="text" label="Programs used for processing the read group (PG)" />
     </xml>
     <xml name="read_group_pi_param">
         <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
     </xml>
     <xml name="read_group_pu_param">
-        <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
+        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
     </xml>
     <xml name="read_group_pu_required_param">
-        <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
+        <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
     </xml>
     <!-- Only ID is required - all groups available -->
     <xml name="read_group_inputs_spec">
diff -r 09a7281d24c5 -r d8c9597bfb09 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 21 14:12:49 2015 -0400
+++ b/tool_dependencies.xml	Tue Nov 03 09:36:45 2015 -0500
@@ -3,7 +3,7 @@
     <package name="bwa" version="0.7.10.039ea20639">
         <repository changeset_revision="5b9aca1e1c07" name="package_bwa_0_7_10_039ea20639" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="samtools" version="1.1">
-        <repository changeset_revision="f0c7bc0159e9" name="package_samtools_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
      </package>
 </tool_dependency>