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comparison tools/mentalist_call/mentalist_call.xml @ 3:4ea71c8e2db0 draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit f161d96d4d4dcd11a53eeda99595d5fd22891612-dirty
author dfornika
date Wed, 11 Apr 2018 14:44:29 -0400
parents d465e81782a3
children af77acce864b
comparison
equal deleted inserted replaced
2:d465e81782a3 3:4ea71c8e2db0
1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.2"> 1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.5">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.2.2">mentalist</requirement> 3 <requirement type="package" version="0.1.5">mentalist</requirement>
4 </requirements> 4 </requirements>
5 <edam_operations>
6 <edam_operation>operation_3840</edam_operation>
7 </edam_operations>
8 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
9 mentalist 6 mentalist
10 call 7 call
11 -o '$output_file' 8 -o '$output_file'
12 --db '$kmer_db.fields.path' 9 --db '$kmer_db.fields.path'
13 --mutation_threshold '$mutation_threshold'
14 --kt '$kmer_threshold'
15 $output_votes
16 $output_special
17 #if $input_type.sPaired == "paired": 10 #if $input_type.sPaired == "paired":
18 -1 $input_type.pInput1 -2 $input_type.pInput2 11 -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2
19 #elif $input_type.sPaired == "collections": 12 #elif $input_type.sPaired == "collections":
20 -1 $input_type.fastq_collection.forward -2 $input_type.fastq_collection.reverse 13 -s $input_type.fastq_collection.name $input_type.fastq_collection.forward $input_type.fastq_collection.reverse
21 #end if 14 #end if
22 ]]></command> 15 ]]></command>
23 <inputs> 16 <inputs>
24 <conditional name="input_type"> 17 <conditional name="input_type">
25 <param name="sPaired" type="select" label="Single Pair or Collection"> 18 <param name="sPaired" type="select" label="Single Pair or Collection">
37 <param name="kmer_db" type="select"> 30 <param name="kmer_db" type="select">
38 <options from_data_table="mentalist_databases"> 31 <options from_data_table="mentalist_databases">
39 <validator type="no_options" message="No MentaLiST databases are available" /> 32 <validator type="no_options" message="No MentaLiST databases are available" />
40 </options> 33 </options>
41 </param> 34 </param>
42 <param name="mutation_threshold" type="integer" label="Mutation threshold"
43 help="Maximum number of mutations when looking for novel alleles."
44 value="6" min="1" max="25" />
45 <param name="kmer_threshold" type="integer" label="Kmer threshold"
46 help="Minimum number of times a kmer is seen to be considered present in the sample."
47 value="10" min="1" max="25" />
48 <param name="output_votes" type="boolean" label="Output votes"
49 argument="--output_votes" truevalue="--output_votes" falsevalue=""
50 help="Outputs the results for the original voting algorithm" />
51 <param name="output_special" type="boolean" label="Output special"
52 argument="--output_special" truevalue="--output_special" falsevalue=""
53 help="Outputs a fasta file with the alleles from special cases such as incomplete coverage, novel and multiple alleles." />
54 </inputs> 35 </inputs>
55 <outputs> 36 <outputs>
56 <data name="output_file" format="tabular" /> 37 <data name="output_file" format="tabular"/>
57 <data name="coverage_file" format="tabular" />
58 </outputs> 38 </outputs>
59 <help><![CDATA[ 39 <help><![CDATA[
60 ]]></help> 40 ]]></help>
61 <citations> 41 <citations>
62 <citation type="doi">10.1101/172858</citation>
63 <citation type="doi">10.1099/mgen.0.000146</citation> 42 <citation type="doi">10.1099/mgen.0.000146</citation>
64 </citations> 43 </citations>
65 </tool> 44 </tool>