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comparison tools/mentalist_call/mentalist_call.xml @ 1:c6a98b93e569 draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 83ebe793451a5ccbfeff873eda359f699e14ae1e
author dfornika
date Sat, 24 Mar 2018 23:12:21 -0400
parents 1d9e3950ce61
children d465e81782a3
comparison
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0:1d9e3950ce61 1:c6a98b93e569
1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.3"> 1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.2">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.1.3">mentalist</requirement> 3 <requirement type="package" version="0.2.2">mentalist</requirement>
4 </requirements> 4 </requirements>
5 <edam_operations>
6 <edam_operation>operation_3840</edam_operation>
7 </edam_operations>
5 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
6 mentalist 9 mentalist
7 call 10 call
8 -o '$output_file' 11 -o '$output_file'
9 --db '$kmer_db.fields.path' 12 --db '$kmer_db.fields.path'
13 --mutation_threshold '$mutation_threshold'
14 --kt '$kmer_threshold'
15 $output_votes
16 $output_special
10 #if $input_type.sPaired == "paired": 17 #if $input_type.sPaired == "paired":
11 -s $input_type.pInput1.name $input_type.pInput1 $input_type.pInput2 18 -s $input_type.pInput1.name -1 $input_type.pInput1 -2 $input_type.pInput2
12 #elif $input_type.sPaired == "collections": 19 #elif $input_type.sPaired == "collections":
13 -s $input_type.fastq_collection.name $input_type.fastq_collection.forward $input_type.fastq_collection.reverse 20 -s $input_type.fastq_collection.name -1 $input_type.fastq_collection.forward -2 $input_type.fastq_collection.reverse
14 #end if 21 #end if
15 ]]></command> 22 ]]></command>
16 <inputs> 23 <inputs>
17 <conditional name="input_type"> 24 <conditional name="input_type">
18 <param name="sPaired" type="select" label="Single Pair or Collection"> 25 <param name="sPaired" type="select" label="Single Pair or Collection">
30 <param name="kmer_db" type="select"> 37 <param name="kmer_db" type="select">
31 <options from_data_table="mentalist_databases"> 38 <options from_data_table="mentalist_databases">
32 <validator type="no_options" message="No MentaLiST databases are available" /> 39 <validator type="no_options" message="No MentaLiST databases are available" />
33 </options> 40 </options>
34 </param> 41 </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." />
35 </inputs> 54 </inputs>
36 <outputs> 55 <outputs>
37 <data name="output_file" format="tabular"/> 56 <data name="output_file" format="tabular" />
57 <data name="coverage_file" format="tabular" />
38 </outputs> 58 </outputs>
39 <help><![CDATA[ 59 <help><![CDATA[
40 ]]></help> 60 ]]></help>
41 <citations> 61 <citations>
42 <citation type="doi">10.1101/172858</citation> 62 <citation type="doi">10.1101/172858</citation>
63 <citation type="doi">10.1099/mgen.0.000146</citation>
43 </citations> 64 </citations>
44 </tool> 65 </tool>