# HG changeset patch
# User mvdbeek
# Date 1483117815 18000
# Node ID a206c60df52807a23ed4baffffbd0146033cf1e3
# Parent  3ffa0a5cbd8ccede6f7da55cb50d653a82be725f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27

diff -r 3ffa0a5cbd8c -r a206c60df528 fermi2.xml
--- a/fermi2.xml	Fri Dec 30 11:56:08 2016 -0500
+++ b/fermi2.xml	Fri Dec 30 12:10:15 2016 -0500
@@ -9,13 +9,13 @@
         -s$genome_size
         -t\${GALAXY_SLOTS:-4}
         -l$readlength
-        -p prefix <(cat
+        -p prefix "
         #for fastq in $input1:
             '$fastq'
         #end for
-        )
-        $T
-        $2
+        "
+        -T $T
+        $two_pass_error
         $E
         > prefix.mak &&
         make -f prefix.mak
@@ -25,7 +25,7 @@
         <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/>
         <param argument="-s" name="genome_size" type="integer" value="180000" min="1" label="approximate genome size in kilobases" help="Enter approximate genome size in kilobases. For a human genome of 3.2 gigabases enter 3200000"/>
         <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/>
-        <param argument="-2" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/>
+        <param argument="-2" name="two_pass_error" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/>
         <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/>
     </inputs>
     <outputs>
@@ -33,7 +33,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="input1" value="test.fastq.gz"/>
+            <param name="input1" value="test.fastq.gz,test.fastq.gz"/>
             <param name="readlength" value="150"/>
             <param name="genome_size" value="1"/>
             <output name="unitigs" file="unitigs.gz" compare="sim_size"/>