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comparison mitokmer.xml @ 1:1434bc7b4786 draft

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planemo upload commit 03463f4b0598df5619def5230de3fb758b4090ba-dirty
author cstrittmatter
date Mon, 22 Apr 2019 09:37:19 -0400
parents 1472b4f4fbfe
children a0852bb4b09b
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0:1472b4f4fbfe 1:1434bc7b4786
27 #set $rev = "R2.fasta.gz" 27 #set $rev = "R2.fasta.gz"
28 #else 28 #else
29 #set $fwd = "R1.fasta" 29 #set $fwd = "R1.fasta"
30 #set $rev = "R2.fasta" 30 #set $rev = "R2.fasta"
31 #end if 31 #end if
32 ln -s $forward $fwd; 32 ln -s $forward $__tool_directory__/process/$fwd;
33 ln -s $reverse $rev; 33 ln -s $reverse $__tool_directory__/process/$rev;
34 #if $reads.reads_select == "single" 34 #if $reads.reads_select == "single"
35 #set $rev = "none" 35 #set $rev = "none"
36 #end if 36 #end if
37 mkdir ./output; 37 mkdir $__tool_directory__/output;
38 python $__tool_directory__/kmer_read_m3.py 38 python $__tool_directory__/kmer_read_m3.py
39 -w $__tool_directory__ 39 -w $__tool_directory__/
40 -d ./output 40 -d $__tool_directory__/output
41 -i $fwd $rev 41 -i $__tool_directory__/process/$fwd $__tool_directory__/process/$rev
42 42
43 ]]></command> 43 ]]></command>
44 <inputs> 44 <inputs>
45 45
46 <conditional name="reads"> 46 <conditional name="reads">