diff samtools_flagstat.xml @ 6:28eb6a47be96 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_flagstat commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

--- a/samtools_flagstat.xml	Fri Dec 18 19:44:33 2015 -0500
+++ b/samtools_flagstat.xml	Tue May 09 11:16:36 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>