diff tools/mira4/mira4_bait.xml @ 18:381aa262c8cb draft

Uploaded v0.0.2 preview 10, override /tmp via environment variable

--- a/tools/mira4/mira4_bait.xml	Mon Mar 03 11:49:21 2014 -0500
+++ b/tools/mira4/mira4_bait.xml	Tue Mar 25 07:37:50 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.1">
+<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.2">
     <description>Filter reads using kmer matches</description>
     <requirements>
         <requirement type="binary">mirabait</requirement>
@@ -31,16 +31,8 @@
                help="How many k-mer matches do you want per read? Minimum one" />
     </inputs>
     <outputs>
-        <data name="output_reads" format="fasta" label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name">
-            <!-- TODO - Replace this with format="input:input_reads" if/when that works -->
-            <change_format>
-                <when input_dataset="input_reads" attribute="extension" value="fastq" format="fastq" />
-                <when input_dataset="input_reads" attribute="extension" value="fastqsanger" format="fastqsanger" />
-                <when input_dataset="input_reads" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-                <when input_dataset="input_reads" attribute="extension" value="fastqillumina" format="fastqillumina" />
-                <when input_dataset="input_reads" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-            </change_format>
-        </data>
+        <data name="output_reads" format="input" metadata_source="input_reads"
+	      label="$input_reads.name #if str($output_choice)=='pos' then 'matching' else 'excluding matches to' # $bait_file.name"/>
     </outputs>
     <tests>
         <test>