# HG changeset patch
# User iuc
# Date 1494343109 14400
# Node ID cc61ade70eb8cf7fb175ba56c1ba8276ce11c0b7
# Parent  0072bf5937917a552e825b265f69ea7dac50fd0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

diff -r 0072bf593791 -r cc61ade70eb8 macros.xml
--- a/macros.xml	Tue Apr 21 15:56:53 2015 -0400
+++ b/macros.xml	Tue May 09 11:18:29 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 0072bf593791 -r cc61ade70eb8 samtools_flagstat.xml
--- a/samtools_flagstat.xml	Tue Apr 21 15:56:53 2015 -0400
+++ b/samtools_flagstat.xml	Tue May 09 11:18:29 2017 -0400
@@ -1,32 +1,37 @@
-<tool id="samtools_flagstat" name="Flagstat" version="2.0">
-  <description>tabulate descriptive stats for BAM datset</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="stdio"></expand>
-  <expand macro="version_command"></expand>
-  <command>samtools flagstat "$input1" > "$output1"
-  </command>
-  <inputs>
-    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
-  </inputs>
-  <outputs>
-    <data name="output1" format="txt" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
-      <output name="output1" file="samtools_flagstat_out1.txt" />
-    </test>
-  </tests>
-  <help>
+<tool id="samtools_flagstat" name="Flagstat" version="2.0.1">
+    <description>tabulate descriptive stats for BAM datset</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+
+    <command><![CDATA[
+        samtools flagstat '$input1' > '$output1'
+    ]]></command>
 
+    <inputs>
+        <param name="input1" type="data" format="bam" label="BAM File to report statistics of" />
+    </inputs>
+
+    <outputs>
+        <data name="output1" format="txt" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input1" value="samtools_flagstat_input1.bam" ftype="bam" />
+            <output name="output1" file="samtools_flagstat_out1.txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Uses ``samtools flagstat`` command to print descriptive information for a BAM dataset. Here is an example of such information::
 
-  200 + 0 in total (QC-passed reads + QC-failed reads)  
+  200 + 0 in total (QC-passed reads + QC-failed reads)
   0 + 0 secondary
   0 + 0 supplementary
   0 + 0 duplicates
@@ -39,7 +44,6 @@
   25 + 0 singletons (12.50%:nan%)
   0 + 0 with mate mapped to a different chr
   0 + 0 with mate mapped to a different chr (mapQ>=5)
-  
-  </help>
-  <expand macro="citations"></expand>
+    ]]></help>
+    <expand macro="citations"/>
 </tool>
diff -r 0072bf593791 -r cc61ade70eb8 test-data/samtools_flagstat_out1.txt
--- a/test-data/samtools_flagstat_out1.txt	Tue Apr 21 15:56:53 2015 -0400
+++ b/test-data/samtools_flagstat_out1.txt	Tue May 09 11:18:29 2017 -0400
@@ -2,12 +2,12 @@
 0 + 0 secondary
 0 + 0 supplementary
 0 + 0 duplicates
-25 + 0 mapped (12.50%:nan%)
+25 + 0 mapped (12.50% : N/A)
 200 + 0 paired in sequencing
 100 + 0 read1
 100 + 0 read2
-0 + 0 properly paired (0.00%:nan%)
+0 + 0 properly paired (0.00% : N/A)
 0 + 0 with itself and mate mapped
-25 + 0 singletons (12.50%:nan%)
+25 + 0 singletons (12.50% : N/A)
 0 + 0 with mate mapped to a different chr
 0 + 0 with mate mapped to a different chr (mapQ>=5)
diff -r 0072bf593791 -r cc61ade70eb8 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 21 15:56:53 2015 -0400
+++ /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="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>