Mercurial > repos > iuc > mykrobe_predict

annotate macro.xml @ 4:a2e3ad69ee23 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
author iuc
date Thu, 26 Aug 2021 20:38:36 +0000
parents e8405163fb4e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
1 <macros>
4
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
2 <token name="@TOOL_VERSION@">0.10.0</token>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
3 <token name="@PROFILE@">20.09</token>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
4 <xml name="requirements">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
5 <requirements>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
6 <requirement type="package" version="@TOOL_VERSION@">mykrobe</requirement>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
7 </requirements>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
8 </xml>
1
60ffb465aa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
parents: 0
diff changeset
9
4
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
10 <token name="@shared_options@">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
11 <![CDATA[
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
12 #if $kmer:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
13 --kmer ${kmer}
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
14 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
15 #if $expected_depth:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
16 --expected_depth ${expected_depth}
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
17 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
18 $ont
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
19 $report_all_calls
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
20 #if $expected_error_rate:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
21 --expected_error_rate ${expected_error_rate}
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
22 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
23 #if $min_variant_conf:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
24 --min_variant_conf ${min_variant_conf}
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
25 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
26 #if $min_gene_conf:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
27 --min_gene_conf ${min_gene_conf}
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
28 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
29 #if $min_proportion_expected_depth:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
30 --min_proportion_expected_depth ${min_proportion_expected_depth}
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
31 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
32 #if $min_gene_percent_covg_threshold:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
33 --min_gene_percent_covg_threshold ${min_gene_percent_covg_threshold}
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
34 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
35 $guess_sequence_method
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
36 $ignore_minor_calls
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
37 #if $ignore_filtered:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
38 --ignore_filtered '${ignore_filtered}'
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
39 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
40 #if $model:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
41 --model '${model}'
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
42 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
43 #if $ploidy:
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
44 --ploidy '${ploidy}'
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
45 #end if
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
46 ]]>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
47 </token>
1
60ffb465aa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
parents: 0
diff changeset
48
4
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
49 <xml name="inputs">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
50 <conditional name="data_type">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
51 <param name="type" type="select" label="Specify the read type.">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
52 <option value="single">Single-end Data</option>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
53 <option value="paired">Paired-end Data</option>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
54 <option value="collection">Collection Paired-end Data</option>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
55 </param>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
56 <when value="single">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
57 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz,bam" label="Single end read file(s)"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
58 </when>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
59 <when value="paired">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
60 <param name="seq1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
61 <param name="seq2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
62 </when>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
63 <when value="collection">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
64 <param name="collection1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" />
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
65 </when>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
66 </conditional>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
67 </xml>
0
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
68
4
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
69 <xml name="options">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
70 <param argument="--kmer" optional="True" type="integer" min="0" label="Kmer length" value="21" help="default = 21"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
71 <param argument="--expected_error_rate" optional="True" type="float" label="Expected error rate" help="Expected sequencing error rate. Set to 0.15 for ONT genotyping"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
72 <param argument="--expected_depth" optional="True" type="integer" min="0" label="Expected depth" help=""/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
73 <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Set default for ONT data" help=""/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
74 <param argument="--min_variant_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for variant genotyping" help=""/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
75 <param argument="--min_gene_conf" optional="True" type="integer" min="0" label="Minimum genotype confidence for gene genotyping" help=""/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
76 <param argument="--min_gene_percent_covg_threshold" optional="True" type="integer" min="0" label="Minimum gene predict coverage" help="all genes alleles found above this percent coverage will be reported (default 100 (only best alleles reported))"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
77 <param argument="--min_proportion_expected_depth" optional="True" type="float" label="Minimum depth required on the sum of both alleles" help="Default 0.3 (30%)"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
78 <param argument="--model" optional="True" type="data" format="txt" label="Genotype model used" help="default kmer_count. Options kmer_count, median_depth"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
79 <param argument="--ploidy" optional="True" type="select" label="Diploid or Haploid" help="Use a diploid (includes 0/1 calls) or haploid genotyping model">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
80 <option value="diploid">diploid</option>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
81 <option value="haploid">haploid</option>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
82 </param>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
83 <param argument="--report_all_calls" type="boolean" truevalue="--report_all_calls" falsevalue="" label="Report all calls" help=""/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
84 <param argument="--ignore_minor_calls" type="boolean" truevalue="--ignore_minor_calls" falsevalue="" label="Ignore minor calls" help="Ignore minor calls when running resistance prediction"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
85 <param argument="--ignore_filtered" type="data" format="txt" label="Ignore filtered" optional="True" help="Don't include filtered genotypes"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
86 <param argument="--guess_sequence_method" type="boolean" truevalue="--guess_sequence_method" falsevalue="" label="Guess sequence method" help="Guess if ONT or Illumia based on error rate. If error rate is > 10%, ploidy is set to haploid and a confidence threshold is used"/>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
87 </xml>
1
60ffb465aa4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 98633f779dfac95f55fbe30519f4e88da0bb9449
iuc
parents: 0
diff changeset
88
4
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
89 <token name="@ATTRIBUTION@">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
90 <![CDATA[
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
91 **MyKrobe predict - Antibiotic resistance predictions**
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
92 Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
93 using Bruijn graph.
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
94 ]]>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
95 </token>
0
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
96
4
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
97 <xml name="citation">
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
98 <citations>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
99 <citation type="doi">10.1038/ncomms10063</citation>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
100 </citations>
a2e3ad69ee23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit 3df97df276e6d3c2800d6f41161b3d7cd8fcbf2a"
iuc
parents: 3
diff changeset
101 </xml>
0
33463c79e697 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe commit deb581240339f3198dc23019e4445e8983ffa6ab
iuc
parents:
diff changeset
102 </macros>