--- a/sampleFasta.xml	Mon Dec 09 04:14:48 2019 -0500
+++ b/sampleFasta.xml	Fri Jan 31 06:55:23 2020 -0500
@@ -1,5 +1,5 @@
-<tool id="sampler" name="Sequence sampling" version="1.0.0">
-  <description> Tool for creating samples of sequences from larger dataset</description>
+<tool id="sampler" name="Read sampling" version="1.0.0">
+  <description> Tool for random sampling subsets of reads from larger dataset</description>
   <requirements>
     <requirement type="package">seqkit</requirement>
   </requirements>
@@ -7,24 +7,26 @@
     <exit_code range="1:" level="fatal" description="Error" />
   </stdio>
   <command>
+    <![CDATA[
     #if str($paired)=="true"
       ${__tool_directory__}/deinterlacer.py $input Afile Bfile
-      &amp;&amp;
-      seqkit sample -2 --number $number --rand-seed $seed -o Asample -w 0 Afile
-      &amp;&amp;
-      seqkit sample -2 --number $number --rand-seed $seed -o Bsample -w 0 Bfile
-      &amp;&amp;
+      &&
+      seqkit sample -2 --number $number --rand-seed $seed -o Asample -w 0 Afile < /dev/null
+      &&
+      seqkit sample -2 --number $number --rand-seed $seed -o Bsample -w 0 Bfile < /dev/null
+      &&
       ${__tool_directory__}/fasta_interlacer.py -a Asample -b Bsample -p $output -x tmpfile
     #else
       seqkit sample -2 --number $number --rand-seed $seed -o $output -w 0 $input
     #end if
-  </command>
+    ]]>
+    </command>
 
   <inputs>
-    <param format="fasta" type="data" name="input" label="Choose your fasta file" />
-    <param name="number" type="integer" size="7" value="500000" min="1" label="number of sequences or sequence pairs"/>
-    <param name="seed" type="integer" size="10" value="10" min="0" label="random number generator seed " />
-    <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="All sequence reads are paired" help="check if you are using pair reads and and input sequences contain both read mates and  left mates alternate with their right mates"/>
+    <param format="fasta" type="data" name="input" label="Read file (FASTA)" />
+    <param name="number" type="integer" size="7" value="500000" min="1" label="Number of reads or read pairs"/>
+    <param name="seed" type="integer" size="10" value="10" min="0" label="Random number generator seed " />
+    <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Paired-end reads" help="If paired-end reads are sampled, left and right-hand reads must be interlaced and all pairs must be complete."/>
     
     
   </inputs>