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comparison seqsero2S.xml @ 1:46d49cf8db7d draft

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planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty
author jpayne
date Wed, 21 Jan 2026 19:30:21 +0000
parents a9790ce778af
children 7a2bd16bd8d9
comparison
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0:a9790ce778af 1:46d49cf8db7d
34 #set $forward = './forward.fastq' 34 #set $forward = './forward.fastq'
35 #end if 35 #end if
36 ln -s $forward ${name}_1.fastq; 36 ln -s $forward ${name}_1.fastq;
37 ln -s $reverse ${name}_2.fastq; 37 ln -s $reverse ${name}_2.fastq;
38 #else 38 #else
39 #set $name = $reads.assembly.name.replace(' ', '_') 39 #set $name = "$reads.assembly.name.replace(' ', '_')"
40 #set $ga = $reads.assembly 40 #set $ga = "$reads.assembly"
41 #set $infile = $name + ".fasta" 41 #set $infile = $name + .fasta
42 ln -s $ga ${name}.fasta; 42 ln -s $ga "$infile";
43 #set $tval = 4 43 #set $tval = 4
44 #set $mode='k' 44 #set $mode='k'
45 #end if 45 #end if
46 echo $name ; 46 echo "$name" ;
47 echo "-=-=-=-=-" ; 47 echo "-=-=-=-=-" ;
48 touch output/SeqSero_log.txt ; 48 touch output/SeqSero_log.txt ;
49 /usr/local/bin/SeqSero2S.py --version ; 49 /usr/local/bin/SeqSero2S.py --version ;
50 echo "-=-=-=-=-" ; 50 echo "-=-=-=-=-" ;
51 /usr/local/bin/SeqSero2S.py 51 /usr/local/bin/SeqSero2S.py
54 -m $mode 54 -m $mode
55 -d ./output 55 -d ./output
56 #if $mode == 'a': 56 #if $mode == 'a':
57 -b $maptype 57 -b $maptype
58 #end if 58 #end if
59 -i $infile && 59 -i "$infile" &&
60 echo "-=-=-=-=-" && 60 echo "-=-=-=-=-" &&
61 cat output/SeqSero_log.txt && 61 cat output/SeqSero_log.txt &&
62 echo "-=-=-=-=-" && 62 echo "-=-=-=-=-" &&
63 ls -lah ./output 63 ls -lah ./output
64 ]]></command> 64 ]]></command>