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comparison tools/mentalist_call/mentalist_call.xml @ 55:30cddbcc549b draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit f8c92831eef76c170c55da87b82697cb44118de8-dirty
author dfornika
date Thu, 24 May 2018 16:58:53 -0400
parents 750c83ff09e5
children ac77718d53b8
comparison
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54:750c83ff09e5 55:30cddbcc549b
1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.2.2"> 1 <tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.8b">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="0.2.2">mentalist</requirement> 3 <requirement type="package" version="0.1.8b">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> 42 <citation type="doi">10.1101/172858</citation>
63 <citation type="doi">10.1099/mgen.0.000146</citation>
64 </citations> 43 </citations>
65 </tool> 44 </tool>