diff bam_to_sam.xml @ 6:eac9d3319326 draft

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

--- a/bam_to_sam.xml	Fri Dec 18 19:42:16 2015 -0500
+++ b/bam_to_sam.xml	Tue May 09 11:17:29 2017 -0400
@@ -1,21 +1,23 @@
-<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0">
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <expand macro="version_command"></expand>
-  <expand macro="stdio"></expand>
-  <description>convert BAM to SAM</description>  
-    <command>
-<![CDATA[
-  samtools view -o "${output1}" ${header} "${input1}"
-]]>
-    </command>
+<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0.1">
+    <description>convert BAM to SAM</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+
+    <command><![CDATA[
+        samtools view -o '${output1}' ${header} '${input1}'
+    ]]></command>
+
     <inputs>
-        <param format="bam" label="BAM File to Convert" name="input1" type="data" />
-        <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
+        <param format="bam" name="input1" type="data" label="BAM File to Convert" />
+        <param name="header" label="Header options" type="select"
+               help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
           <option value="-h">Include header in SAM output (-h)</option>
-          <option value="-H">Print header only (-H)</option>
+          <option value="-H">Return header only (-H)</option>
           <option value="">Exclude header</option>
         </param>
     </inputs>
@@ -26,29 +28,23 @@
         <test>
             <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
             <param name="header" value="-h" />
-            <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
+            <output file="bam_to_sam_out1.sam" name="output1" />
         </test>
         <test>
             <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
             <param name="header" value="-H" />
-            <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
+            <output file="bam_to_sam_out2.sam" name="output1" />
         </test>
         <test>
             <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
             <param name="header" value="" />
-            <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
+            <output file="bam_to_sam_out3.sam" name="output1" />
         </test>
     </tests>
-    <help>
-<![CDATA[
-
+    <help><![CDATA[
 **What it does**
 
-Converts BAM dataset to SAM using ``samtools view`` command::
-
- samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] 
-
-]]>
-  </help>
-  <expand macro="citations"></expand>
+Converts BAM dataset to SAM using the ``samtools view`` command.
+    ]]></help>
+    <expand macro="citations"/>
 </tool>