# HG changeset patch
# User iuc
# Date 1494343083 14400
# Node ID 6166013090c0dab715957b716dfe9b9e4ec3a122
# Parent  8bfe0d1616d2106783aa1b2cf36c5adcffc48952
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

diff -r 8bfe0d1616d2 -r 6166013090c0 macros.xml
--- a/macros.xml	Wed Nov 11 12:53:49 2015 -0500
+++ b/macros.xml	Tue May 09 11:18:03 2017 -0400
@@ -1,16 +1,17 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.2">samtools</requirement>
+            <requirement type="package" version="1.3.1">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
+    <token name="@TOOL_VERSION@">1.3.1</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
                 @misc{SAM_def,
                 title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+                url = {https://samtools.github.io/hts-specs/},}
             </citation>
             <citation type="doi">10.1093/bioinformatics/btp352</citation>
             <citation type="doi">10.1093/bioinformatics/btr076</citation>
@@ -41,7 +42,7 @@
         </citations>
     </xml>
     <xml name="version_command">
-        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
     </xml>
     <xml name="stdio">
         <stdio>
@@ -64,7 +65,5 @@
 5. Click **Save**
 
 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
-
     </token>
-
 </macros>
diff -r 8bfe0d1616d2 -r 6166013090c0 samtools_phase.xml
--- a/samtools_phase.xml	Wed Nov 11 12:53:49 2015 -0500
+++ b/samtools_phase.xml	Tue May 09 11:18:03 2017 -0400
@@ -1,12 +1,13 @@
-<tool id="samtools_phase" name="Call and phase" version="2.0">
+<tool id="samtools_phase" name="Call and phase" version="2.0.1">
     <description>heterozygous SNPs</description>
     <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio"></expand>
-  <expand macro="version_command"></expand>
-    <command>samtools phase -b "phase_wrapper"
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+    samtools phase -b phase_wrapper
         #if str($option_set.option_sets) == 'advanced':
             ${option_set.ignore_chimeras}
             -k $option_set.block_length
@@ -15,10 +16,13 @@
             -D $option_set.read_depth
             ${option_set.drop_ambiguous}
         #else
-            -k 13 -q 37 -Q 13 -D 256
+            -k 13
+            -q 37
+            -Q 13
+            -D 256
         #end if
-        "$input_bam" &gt; "$phase_sets"
-    </command>
+        '$input_bam' > '$phase_sets'
+    ]]></command>
     <inputs>
         <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
         <conditional name="option_set">
@@ -28,12 +32,12 @@
             </param>
             <when value="default" />
             <when value="advanced">
-                <param name="block_length" type="integer" value="13" label="Maximum length for local phasing" />
-                <param name="min_het" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
-                <param name="min_bq" type="integer" value="13" label="Minimum base quality to be used in het calling" />
-                <param name="read_depth" type="integer" value="256" label="Read depth" />
-                <param name="ignore_chimeras" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
-                <param name="drop_ambiguous" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
+                <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" />
+                <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
+                <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" />
+                <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" />
+                <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
+                <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
             </when>
         </conditional>
     </inputs>
@@ -81,50 +85,10 @@
             <output name="chimera" file="empty_file.bam" compare="contains" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
-Call and phase heterozygous SNPs
-    
-------
-
-.. list-table:: **Options**
-   :widths: 5 5 40 10
-   :header-rows: 1
-
-   * - Flag
-     - Type
-     - Description
-     - Default
-   * - -k
-     - INT
-     - Block length
-     - 13
-   * - -b
-     - STR
-     - Prefix of BAM file output
-     - *null*
-   * - -q
-     - INT
-     - Minimum het phred-LOD
-     - 37
-   * - -Q
-     - INT
-     - Min base quality in het calling
-     - 13
-   * - -D
-     - INT
-     - Max read depth
-     - 256
-   * - -D
-     - BOOLEAN
-     - Do not attempt to fix chimeras
-     - *off*
-   * - -A
-     - BOOLEAN
-     - Drop reads with ambiguous phase
-     - *off*
-
-    </help>
-    <expand macro="citations"></expand>
+Call and phase heterozygous SNPs.
+    ]]></help>
+    <expand macro="citations"/>
 </tool>
diff -r 8bfe0d1616d2 -r 6166013090c0 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Nov 11 12:53:49 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <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>