Commit 68bfd33f authored by JCabral's avatar JCabral

fix output for paired collection

parent 0d985c0b
......@@ -11,19 +11,17 @@
#if $single_or_paired.type == "single"
single
$input_se
$coverage $output
#elif $single_or_paired.type == "paired"
paired
$single_or_paired.forward_pe $single_or_paired.reverse_pe
$coverage $output $output_rev
#else
collection
$single_or_paired.fastq_collection.forward $single_or_paired.fastq_collection.reverse
$coverage $output_collection.forward $output_collection.reverse
#end if
$coverage $output
#if $single_or_paired.type != "single"
$output_rev
#end if
</command>
<stdio>
<exit_code range="1:" level="fatal" description="Unknown error has occured"/>
......@@ -52,10 +50,18 @@
</inputs>
<outputs>
<data format="fastqsanger" name="output" label="SubSampled Fastq" />
<data format="fastqsanger" name="output" label="SubSampled Fastq" >
<filter>single_or_paired['type']!="collection"</filter>
</data>
<data format="fastqsanger" name="output_rev" label="SubSampled Fastq Reverse">
<filter>single_or_paired['type']!="single"</filter>
<filter>single_or_paired['type']=="paired"</filter>
</data>
<collection name="output_collection" type="paired" label="SubSampled Fastqs">
<data name="forward" format="fastqsanger"/>
<data name="reverse" format="fastqsanger"/>
<filter>single_or_paired['type']=="collection"</filter>
</collection>
</outputs>
<tests>
......
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