Mercurial > repos > iuc > mykrobe_genotype

comparison mykrobe_genotype.xml @ 1:84f769706f7a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
author iuc
date Tue, 02 Apr 2019 11:57:05 -0400
parents d783eb846f59
children 0f4a5de7878a
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0:d783eb846f59 1:84f769706f7a
1 <?xml version="1.0" encoding="utf-8"?> 1 <tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.6.1" >
2 <tool id="mykrobe_genotype" name="mkyrobe genotype" version="0.5.6" >
3 <description>Antibiotic resistance predictions</description> 2 <description>Antibiotic resistance predictions</description>
4 <macros> 3 <macros>
5 <import>macro.xml</import> 4 <import>macro.xml</import>
6 </macros> 5 </macros>
7 <expand macro="requirements"/> 6 <expand macro="requirements"/>
8 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code">
9 <![CDATA[ 8 <![CDATA[
10 @select_inputs@ 9 @select_inputs@
11 10
12 mykrobe genotype 11 mykrobe genotype
13 '$name' 12 '${name}'
14 '$probe_set' 13 '${probe_set}'
15 14
16 #if $kmer: 15 #if $filter:
17 --kmer $kmer 16 --filters '${filter}'
18 #end if 17 #end if
19 18
20 #if $expected_depth: 19 @shared_options@
21 --expected_depth $expected_depth
22 #end if
23
24 20
25 -q 21 -q
26 -t "\${GALAXY_SLOTS:-1}" 22 -t "\${GALAXY_SLOTS:-1}"
27 23
28 -1 24 -1
31 #elif $type == 'bam': 27 #elif $type == 'bam':
32 *.bam 28 *.bam
33 #else 29 #else
34 *.fasta 30 *.fasta
35 #end if 31 #end if
36 > $json 32 > '$json'
37 ]]> 33 ]]>
38 </command> 34 </command>
39 <inputs> 35 <inputs>
40 <expand macro="inputs" /> 36 <expand macro="inputs" />
41 <param name="probe_set" type="data" format="fasta" label="Probe Set"/> 37 <param argument="--probe_set" type="data" format="fasta" label="Probe Set"/>
42 <param name="kmer" argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/> 38 <param argument="--filter" type="data" format="txt,fasta" label="Filter Genotypes" optional="True" help="Don't include filtered genotypes"/>
43 <param name="expected_depth" argument="--expected_depth" optional="True" type="integer" min="0" label="Expected Depth" help=""/> 39 <expand macro="options"/>
44 </inputs> 40 </inputs>
45 <outputs> 41 <outputs>
46 <data name="json" format="json" label="JSON prediction"/> 42 <data name="json" format="json" label="JSON prediction"/>
47 </outputs> 43 </outputs>
48 <tests> 44 <tests>