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comparison seqsero2S.xml @ 3:5ca386f1720d draft

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planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty
author jpayne
date Tue, 21 Apr 2026 15:46:51 +0000
parents 7a2bd16bd8d9
children 50f9648ed5c0
comparison
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2:7a2bd16bd8d9 3:5ca386f1720d
1 <tool id="seqsero2s" name="SeqSero2S" version="1"> 1 <tool id="seqsero2s" name="SeqSero2S" version="1.1.4">
2 <description>Simplified Salmonella serotype prediction</description> 2 <description>Simplified Salmonella serotype prediction</description>
3 <requirements> 3 <requirements>
4 <!-- <requirement type="package" version="@VERSION@">seqsero2s</requirement> --> 4 <!-- <requirement type="package" version="@VERSION@">seqsero2s</requirement> -->
5 <container type="docker">quay.io/biocontainers/seqsero2s:1.1.3--pyhdfd78af_0</container> 5 <container type="docker">quay.io/biocontainers/seqsero2s:1.1.4--pyhdfd78af_1</container>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir ./output; 8 mkdir ./output;
9 9
10 #if $reads.reads_select == 'history' 10 #if $reads.reads_select == 'history'
31 gunzip -c $reverse > reverse.fastq; 31 gunzip -c $reverse > reverse.fastq;
32 #set $reverse = './reverse.fastq' 32 #set $reverse = './reverse.fastq'
33 gunzip -c $forward > forward.fastq; 33 gunzip -c $forward > forward.fastq;
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 $infile = $name + ".fasta" 40 #set $infile = $name + ".fasta"
41 ln -s $reads.assembly "$infile"; 41 ln -s $reads.assembly "$infile";
42 #set $tval = 4 42 #set $tval = 4
43 #set $mode='k' 43 #set $mode='k'
44 #end if 44 #end if
45 echo "$name" ; 45 echo "$name" ;
46 echo "-=-=-=-=-" ; 46 echo "-=-=-=-=-" ;
47 touch output/SeqSero_log.txt ; 47 touch output/data_log.txt ;
48 /usr/local/bin/SeqSero2S.py --version ; 48 /usr/local/bin/SeqSero2S.py --version ;
49 echo "-=-=-=-=-" ; 49 echo "-=-=-=-=-" ;
50 /usr/local/bin/SeqSero2S.py 50 /usr/local/bin/SeqSero2S.py
51 -p \${GALAXY_SLOTS:-1} 51 -p \${GALAXY_SLOTS:-1}
52 -t $tval 52 -t $tval
53 -m $mode 53 -m $mode
54 -d ./output 54 -d ./output
55 #if $mode == 'a': 55 #if $mode == 'a':
56 -b $maptype 56 -b $maptype
57 #end if 57 #end if
58 -i "$infile" && 58 -i $infile &&
59 echo "-=-=-=-=-" && 59 echo "-=-=-=-=-" ;
60 cat output/SeqSero_log.txt && 60 cat output/data_log.txt &&
61 echo "-=-=-=-=-" && 61 echo "-=-=-=-=-" &&
62 ls -lah ./output 62 ls -lah ./output
63 ]]></command> 63 ]]></command>
64 <inputs> 64 <inputs>
65 65