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comparison nanopolish_variants.xml @ 7:32cb27adeb34 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
author jdv
date Mon, 12 Feb 2018 00:58:10 -0500
parents 36cc4ae4160e
children f1141f6a2d65
comparison
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6:36cc4ae4160e 7:32cb27adeb34
1 <tool id="nanopolish_variants" name="Nanopolish::variants" version="0.8.2"> 1 <tool id="nanopolish_variants" name="Nanopolish::variants" version="0.8.5">
2 2
3 <description>Re-call consensus and variants from raw signal</description> 3 <description>Re-call consensus and variants from raw signal</description>
4 4
5 <!-- ***************************************************************** --> 5 <!-- ***************************************************************** -->
6 6
7 <!--
8 <requirements> 7 <requirements>
9 <requirement type="package" version="0.7.2">nanopolish</requirement> 8 <requirement type="package" version="0.8.5">nanopolish</requirement>
10 </requirements> 9 </requirements>
11 -->
12 10
13 <!-- ***************************************************************** --> 11 <!-- ***************************************************************** -->
14 12
15 <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command> 13 <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
16 14
33 --max-rounds $max_rounds 31 --max-rounds $max_rounds
34 --max-haplotypes $max_haplotypes 32 --max-haplotypes $max_haplotypes
35 --min-candidate-depth $min_candidate_depth 33 --min-candidate-depth $min_candidate_depth
36 --min-candidate-frequency $min_candidate_frequency 34 --min-candidate-frequency $min_candidate_frequency
37 --fast5 $input_fast5 35 --fast5 $input_fast5
36 #if $input_index:
37 --index $input_index
38 #end if
38 $fix_homopolymers 39 $fix_homopolymers
39 $calculate_all_support 40 $calculate_all_support
40 41
41 ]]> 42 ]]>
42 </command> 43 </command>
43 44
44 <!-- ***************************************************************** --> 45 <!-- ***************************************************************** -->
45 46
46 <inputs> 47 <inputs>
47 48
48 <param name="input_reads" type="data" format="fasta" label="Input reads (FASTA)" /> 49 <param name="input_reads" type="data" format="fasta,fastq" label="Input reads (FASTA/Q)" />
49 <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" /> 50 <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" />
50 <param name="input_bam" type="data" format="bam" label="Alignment" /> 51 <param name="input_bam" type="data" format="bam" label="Alignment" />
51 <param name="input_ref" type="data" format="fasta" label="Reference" /> 52 <param name="input_ref" type="data" format="fasta" label="Reference" />
53 <param name="input_index" type="data" format="tar" label="Precalculated index (optional)" optional="True" />
52 <param name="min_candidate_frequency" type="float" value="0.2" size="5" label="Minimum candidate frequency" /> 54 <param name="min_candidate_frequency" type="float" value="0.2" size="5" label="Minimum candidate frequency" />
53 <param name="min_candidate_depth" type="integer" min="1" value="20" size="5" label="Minimum candidate depth" /> 55 <param name="min_candidate_depth" type="integer" min="1" value="20" size="5" label="Minimum candidate depth" />
54 <param name="max_haplotypes" type="integer" min="0" value="1000" size="5" label="Maximum haplotype combinations" /> 56 <param name="max_haplotypes" type="integer" min="0" value="1000" size="5" label="Maximum haplotype combinations" />
55 <param name="max_rounds" type="integer" min="0" value="50" size="5" label="Maximum iterations" /> 57 <param name="max_rounds" type="integer" min="0" value="50" size="5" label="Maximum iterations" />
56 <param name="fix_homopolymers" type="boolean" checked="false" truevalue="--fix-homopolymers" falsevalue="" label="Fix homopolymers" /> 58 <param name="fix_homopolymers" type="boolean" checked="false" truevalue="--fix-homopolymers" falsevalue="" label="Fix homopolymers" />
67 </outputs> 69 </outputs>
68 70
69 <!-- ***************************************************************** --> 71 <!-- ***************************************************************** -->
70 72
71 <tests> 73 <tests>
74 <!-- test defaults with FASTA input -->
72 <test> 75 <test>
73 <param name="input_reads" value="variants.reads.fa" ftype="fasta" /> 76 <param name="input_reads" value="called.fa" ftype="fasta" />
74 <param name="input_fast5" value="variants.in.fast5.tar.bz2" ftype="fast5.tar.bz2" /> 77 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
75 <param name="input_bam" value="variants.bam" ftype="bam" /> 78 <param name="input_bam" value="called.bam" ftype="bam" />
76 <param name="input_ref" value="variants.ref.fa" ftype="fasta" /> 79 <param name="input_ref" value="ref.fa" ftype="fasta" />
80 <param name="fix_homopolymers" value="False"/>
81 <output name="out_consensus" file="consensus.fa" compare="diff" />
82 <output name="out_variants" file="consensus.vcf" compare="diff" />
83 <assert_command>
84 <not_has_text text="--index" />
85 <not_has_text text="--fix-homopolymers" />
86 </assert_command>
87 </test>
88 <!-- test FASTQ input -->
89 <test>
90 <param name="input_reads" value="called.fq" ftype="fastq" />
91 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
92 <param name="input_bam" value="called.bam" ftype="bam" />
93 <param name="input_ref" value="ref.fa" ftype="fasta" />
94 <param name="fix_homopolymers" value="False"/>
95 <output name="out_consensus" file="consensus.fa" compare="diff" />
96 <output name="out_variants" file="consensus.vcf" compare="diff" />
97 </test>
98 <!-- test homopolymer fixing -->
99 <test>
100 <param name="input_reads" value="called.fa" ftype="fasta" />
101 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
102 <param name="input_bam" value="called.bam" ftype="bam" />
103 <param name="input_ref" value="ref.fa" ftype="fasta" />
77 <param name="fix_homopolymers" value="True"/> 104 <param name="fix_homopolymers" value="True"/>
78 <output name="out_consensus" file="variants.out.fa" compare="diff" /> 105 <output name="out_consensus" file="consensus.hp.fa" compare="diff" />
106 <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
107 </test>
108 <!-- test pre-calculated index input -->
109 <test>
110 <param name="input_reads" value="called.fa" ftype="fasta" />
111 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
112 <param name="input_bam" value="called.bam" ftype="bam" />
113 <param name="input_ref" value="ref.fa" ftype="fasta" />
114 <param name="input_index" value="index.tar" ftype="tar" />
115 <param name="fix_homopolymers" value="True"/>
116 <output name="out_consensus" file="consensus.hp.fa" compare="diff" />
117 <output name="out_variants" file="consensus.hp.vcf" compare="diff" />
118 <assert_command>
119 <has_text text="--index" />
120 <has_text text="--fix-homopolymers" />
121 </assert_command>
79 </test> 122 </test>
80 </tests> 123 </tests>
81 124
82 <!-- ***************************************************************** --> 125 <!-- ***************************************************************** -->
83 126