| Previous changeset 0:a9790ce778af (2025-09-29) Next changeset 2:7a2bd16bd8d9 (2026-01-21) |
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Commit message:
planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty |
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modified:
seqsero2S.xml |
| b |
| diff -r a9790ce778af -r 46d49cf8db7d seqsero2S.xml --- a/seqsero2S.xml Mon Sep 29 20:04:28 2025 +0000 +++ b/seqsero2S.xml Wed Jan 21 19:30:21 2026 +0000 |
| b |
| @@ -36,14 +36,14 @@ ln -s $forward ${name}_1.fastq; ln -s $reverse ${name}_2.fastq; #else - #set $name = $reads.assembly.name.replace(' ', '_') - #set $ga = $reads.assembly - #set $infile = $name + ".fasta" - ln -s $ga ${name}.fasta; + #set $name = "$reads.assembly.name.replace(' ', '_')" + #set $ga = "$reads.assembly" + #set $infile = $name + .fasta + ln -s $ga "$infile"; #set $tval = 4 #set $mode='k' #end if - echo $name ; + echo "$name" ; echo "-=-=-=-=-" ; touch output/SeqSero_log.txt ; /usr/local/bin/SeqSero2S.py --version ; @@ -56,7 +56,7 @@ #if $mode == 'a': -b $maptype #end if - -i $infile && + -i "$infile" && echo "-=-=-=-=-" && cat output/SeqSero_log.txt && echo "-=-=-=-=-" && |