Mercurial > repos > jpayne > seqsero_v2

comparison seqsero2.xml @ 17:03f7b358d57f

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planemo upload
author jpayne
date Tue, 25 Mar 2025 23:22:38 -0400
parents 3b6d5b60968f
children a573df21536d
comparison
equal deleted inserted replaced
16:3b6d5b60968f 17:03f7b358d57f
1 <tool id="seqsero_v2" name="SeqSero2 v1.2.1" version="8"> 1 <tool id="seqsero_v2" name="SeqSero2 v1.3.1" version="8">
2 <description>Salmonella serotype prediction</description> 2 <description>Salmonella serotype prediction</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">1.2.1</token> 4 <token name="@VERSION@">1.3.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@VERSION@">seqsero2</requirement> 7 <requirement type="package" version="@VERSION@">seqsero2</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 echo "SeqSero2 v1.2.1";
11 mkdir ./output; 10 mkdir ./output;
12 11
13 #if $reads.reads_select == 'history' 12 #if $reads.reads_select == 'history'
14 #set $name = $reads.forward.name.split('.')[0].replace(' ','_') 13 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
15 #set $forward = $reads.forward 14 #set $forward = $reads.forward
47 #set $mode='k' 46 #set $mode='k'
48 #end if 47 #end if
49 echo $name ; 48 echo $name ;
50 echo "-=-=-=-=-" ; 49 echo "-=-=-=-=-" ;
51 touch output/SeqSero_log.txt ; 50 touch output/SeqSero_log.txt ;
51 SeqSero2_package.py --version ;
52 echo "-=-=-=-=-" ;
52 SeqSero2_package.py 53 SeqSero2_package.py
53 -p \${GALAXY_SLOTS:-1} 54 -p \${GALAXY_SLOTS:-1}
54 -t $tval 55 -t $tval
55 -m $mode 56 -m $mode
56 -d ./output 57 -d ./output
104 105
105 106
106 107
107 </inputs> 108 </inputs>
108 <outputs> 109 <outputs>
109 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv"/> 110 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv" />
110 </outputs> 111 </outputs>
111 <tests> 112 <tests>
112 <!-- <test> 113 <!-- <test>
113 <param name="reads_select" value="history" /> 114 <param name="reads_select" value="history" />
114 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" /> 115 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
147 <param name="mode" value="a" /> 148 <param name="mode" value="a" />
148 <param name="reads_select" value="history" /> 149 <param name="reads_select" value="history" />
149 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" /> 150 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
150 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" /> 151 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
151 <assert_stdout> 152 <assert_stdout>
152 <has_text text="predicted antigenic profile does not exist" /> 153 <has_text text="input genome cannot be identified as Salmonella" />
153 </assert_stdout> 154 </assert_stdout>
154 </test> 155 </test>
155 <!-- <test> 156 <!-- <test>
156 <param name="mode" value="a" /> 157 <param name="mode" value="a" />
157 <param name="reads_select" value="collection" /> 158 <param name="reads_select" value="collection" />