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comparison legsta.xml @ 1:579f1cabfe79 draft

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"planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
author iuc
date Wed, 09 Mar 2022 20:49:51 +0000
parents b469f6d53d06
children 0411fca1d681
comparison
equal deleted inserted replaced
0:b469f6d53d06 1:579f1cabfe79
1 <tool id="legsta" name="legsta" version="@TOOL_VERSION@" profile="20.01"> 1 <tool id="legsta" name="legsta" version="@TOOL_VERSION@+galaxy1" profile="20.01">
2 <description>Legionella pneumophila sequence based typing</description> 2 <description>Legionella pneumophila sequence based typing</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 8
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 #import re
11 #set safe_names=[]
12
13 #for $i in $contigs
14 #set safe_name=re.sub('[^\s\w\-.]', '_', str($i.element_identifier))
15 $safe_names.append($safe_name)
16 ln -s '$i' '$safe_name';
17 #end for
18
10 legsta 19 legsta
11 20
12 $noheader 21 $noheader
13 $csv 22 $csv
14 23
15 #for $i in $contigs 24 #for $safe_name in $safe_names
16 '$i' 25 '$safe_name'
17 #end for 26 #end for
18 27
19 > '$output' 28 > '$output'
20 ]]></command> 29 ]]></command>
21 30
39 <param name="contigs" ftype="fasta" value="NC_006368.fna.bz2"/> 48 <param name="contigs" ftype="fasta" value="NC_006368.fna.bz2"/>
40 <param name="csv" value="true"/> 49 <param name="csv" value="true"/>
41 <output name="output"> 50 <output name="output">
42 <assert_contents> 51 <assert_contents>
43 <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" /> 52 <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" />
44 <has_text text="1,1,4,3,1,1,1,1" /> 53 <has_text text="NC_006368.fna.bz2,1,1,4,3,1,1,1,1" />
45 </assert_contents> 54 </assert_contents>
46 </output> 55 </output>
47 </test> 56 </test>
48 </tests> 57 </tests>
49 58