diff bamsort.xml @ 5:bdd1995c9e66

upgrade to mimodd version 0.1.6.1

--- a/bamsort.xml	Thu Jun 04 17:52:04 2015 +0200
+++ b/bamsort.xml	Tue Jul 28 23:21:11 2015 +0200
@@ -1,4 +1,4 @@
-<tool id="bamsort" name="Sort BAM file">
+<tool id="bamsort" name="Sort BAM file" version="0.1.6.1">
   <description>Sort a BAM file by coordinates (or names) of the mapped reads</description>
   <macros>
     <import>toolshed_macros.xml</import>
@@ -6,13 +6,27 @@
   <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
-	mimodd sort "$inputfile" -o "$output" --oformat $oformat $by_name
+	mimodd sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name
   </command>
   
   <inputs>
-    <param name="inputfile" type="data" format="bam" label="Input file to sort" />
+    <conditional name="input">
+      <param name="iformat" type="select" label = "Input data format">
+        <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" />
+      </when>
+      <when value="sam">
+        <param name="ifile" type="data" format="sam" label="SAM input file to sort" />
+      </when>
+    </conditional>
+    <param name="oformat" type="select" label = "Output format for the sorted data">
+      <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 name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" />
   </inputs>
   
   <outputs>