diff bamsort.xml @ 23:5db0545b9004 draft

update to v0.1.7.3

--- a/bamsort.xml	Sun Jun 12 07:39:46 2016 -0400
+++ b/bamsort.xml	Thu Jul 21 03:55:49 2016 -0400
@@ -1,9 +1,9 @@
-<tool id="bamsort" name="Sort BAM file" version="0.1.7.2">
+<tool id="bamsort" name="Sort BAM file" version="0.1.7.3">
   <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
   <macros>
     <import>toolshed_macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
+  <expand macro="requirements" />
   <version_command>python3 -m MiModD version -q</version_command>
   <command>
 	python3 -m MiModD sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name
@@ -11,28 +11,28 @@
   
   <inputs>
     <conditional name="input">
-      <param name="iformat" type="select" label = "Input data format">
+      <param label="Input data format" name="iformat" type="select">
         <option value="bam">bam</option>
         <option value="sam">sam</option>
       </param>
       <when value="bam">
-        <param name="ifile" type="data" format="bam" label="BAM input file to sort" />
+        <param format="bam" label="BAM input file to sort" name="ifile" type="data" />
       </when>
       <when value="sam">
-        <param name="ifile" type="data" format="sam" label="SAM input file to sort" />
+        <param format="sam" label="SAM input file to sort" name="ifile" type="data" />
       </when>
     </conditional>
-    <param name="oformat" type="select" label = "Output format for the sorted data">
+    <param label="Output format for the sorted data" name="oformat" type="select">
       <option value="bam">bam</option>
       <option value="sam">sam</option>
     </param>
-    <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." />
+    <param checked="false" falsevalue="" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." label="Sort by read names instead of coordinates" name="by_name" truevalue="-n" type="boolean" />
   </inputs>
   
   <outputs>
-    <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}">
+    <data format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}" name="output">
       <change_format>
-	 <when input="oformat" value="sam" format="sam" />
+	 <when format="sam" input="oformat" value="sam" />
       </change_format>
     </data>
   </outputs>
@@ -49,5 +49,4 @@
 The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem.
 
 </help>
-</tool>
-
+</tool>
\ No newline at end of file