Mercurial > repos > jpayne > seqsero2s
changeset 3:5ca386f1720d draft
planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty
| author | jpayne |
|---|---|
| date | Tue, 21 Apr 2026 15:46:51 +0000 |
| parents | 7a2bd16bd8d9 |
| children | 50f9648ed5c0 |
| files | seqsero2S.xml |
| diffstat | 1 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/seqsero2S.xml Wed Jan 21 20:40:57 2026 +0000 +++ b/seqsero2S.xml Tue Apr 21 15:46:51 2026 +0000 @@ -1,8 +1,8 @@ -<tool id="seqsero2s" name="SeqSero2S" version="1"> +<tool id="seqsero2s" name="SeqSero2S" version="1.1.4"> <description>Simplified Salmonella serotype prediction</description> <requirements> <!-- <requirement type="package" version="@VERSION@">seqsero2s</requirement> --> - <container type="docker">quay.io/biocontainers/seqsero2s:1.1.3--pyhdfd78af_0</container> + <container type="docker">quay.io/biocontainers/seqsero2s:1.1.4--pyhdfd78af_1</container> </requirements> <command detect_errors="exit_code"><![CDATA[ mkdir ./output; @@ -33,8 +33,8 @@ gunzip -c $forward > forward.fastq; #set $forward = './forward.fastq' #end if - ln -s $forward ${name}_1.fastq; - ln -s $reverse ${name}_2.fastq; + ln -s $forward "${name}_1.fastq"; + ln -s $reverse "${name}_2.fastq"; #else #set $name = $reads.assembly.name.replace(' ', '_') #set $infile = $name + ".fasta" @@ -44,7 +44,7 @@ #end if echo "$name" ; echo "-=-=-=-=-" ; - touch output/SeqSero_log.txt ; + touch output/data_log.txt ; /usr/local/bin/SeqSero2S.py --version ; echo "-=-=-=-=-" ; /usr/local/bin/SeqSero2S.py @@ -55,9 +55,9 @@ #if $mode == 'a': -b $maptype #end if - -i "$infile" && - echo "-=-=-=-=-" && - cat output/SeqSero_log.txt && + -i $infile && + echo "-=-=-=-=-" ; + cat output/data_log.txt && echo "-=-=-=-=-" && ls -lah ./output ]]></command>