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comparison seqsero2.xml @ 1:b747b2c8fdb6 draft default tip

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planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty
author jpayne
date Thu, 18 Sep 2025 22:57:05 +0000
parents 225680ef4cc1
children
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0:225680ef4cc1 1:b747b2c8fdb6
1 <tool id="seqsero_v2" name="SeqSero2 v1.3.1" version="9"> 1 <tool id="seqsero_v2" name="SeqSero2 v1.3.1" version="9">
2 <description>Salmonella serotype prediction</description> 2 <description>Salmonella serotype prediction</description>
3 <macros>
4 <token name="@VERSION@">1.3.1</token>
5 </macros>
6 <requirements> 3 <requirements>
7 <!-- <requirement type="package" version="@VERSION@">seqsero2</requirement> --> 4 <!-- <requirement type="package" version="@VERSION@">seqsero2</requirement> -->
8 <container> 5 <container type="docker">quay.io/biocontainers/seqsero2:1.3.1--pyhdfd78af_1</container>
9 <image>seqsero2:1.3.1</image>
10 </container>
11 </requirements> 6 </requirements>
12 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
13 mkdir ./output; 8 mkdir ./output;
14 9
15 #if $reads.reads_select == 'history' 10 #if $reads.reads_select == 'history'
49 #set $mode='k' 44 #set $mode='k'
50 #end if 45 #end if
51 echo $name ; 46 echo $name ;
52 echo "-=-=-=-=-" ; 47 echo "-=-=-=-=-" ;
53 touch output/SeqSero_log.txt ; 48 touch output/SeqSero_log.txt ;
54 SeqSero2_package.py --version ; 49 /usr/local/bin/SeqSero2_package.py --version ;
55 echo "-=-=-=-=-" ; 50 echo "-=-=-=-=-" ;
56 SeqSero2_package.py 51 /usr/local/bin/SeqSero2_package.py
57 -p \${GALAXY_SLOTS:-1} 52 -p \${GALAXY_SLOTS:-1}
58 -t $tval 53 -t $tval
59 -m $mode 54 -m $mode
60 -d ./output 55 -d ./output
61 #if $mode == 'a': 56 #if $mode == 'a':