Mercurial > repos > iuc > tracy_decompose

comparison tracy_decompose.xml @ 0:6d4fa8880e60 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
author iuc
date Tue, 12 Oct 2021 14:18:15 +0000
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1 <tool id="tracy_decompose" name="tracy Decompose" version="@TOOL_VERSION@+galaxy0" profile="20.09">
2 <description>heterozygous mutations (and call variants)</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[
9 #if $index_genome == True
10 bgzip -c '$genome' > genome.fasta.gz ;
11 tracy index -o genome.fasta.fm9 genome.fasta.gz &&
12 #set refgenome = "genome.fasta.gz"
13 #else
14 #set refgenome = $genome
15 #end if
16 tracy decompose
17 --genome '$refgenome'
18 $callVariants
19 --pratio $pratio
20 --kmer $kmer.kmer
21 --support $kmer.support
22 --maxindel $maxindel
23 --trim $trim.trim
24 --trimLeft $trim.trimLeft
25 --trimRight $trim.trimRight
26 --linelimit $linelimit
27 --gapopen $alignment.gapopen
28 --gapext $alignment.gapext
29 --match $alignment.match
30 --mismatch $alignment.mismatch
31 '$tracefile'
32 ]]></command>
33 <inputs>
34 <param argument="--genome" type="data" format="fasta,ab1,scf" label="FASTA, ABI or SCF format genome" />
35 <param name="tracefile" type="data" format="ab1,scf" label="Sanger chromatogram tracefile to align" />
36 <param name="index_genome" type="boolean" label="Pre-index the reference" help="Pre-indexing builds a FM index of the reference. This is required for sequences larger than 50 kilobases" />
37 <param argument="--callVariants" type="boolean" truevalue="--callVariants" falsevalue="" label="Call variants in chromatogram" />
38 <!-- annotate option is not yet supported -->
39 <expand macro="common_options" />
40 <expand macro="kmer_options" />
41 <expand macro="alignment_options" />
42 <expand macro="trim_options" />
43 <expand macro="optional_outputs" />
44 </inputs>
45 <outputs>
46 <expand macro="json_output" toolname="decompose" />
47 <data name="out_fasta1" format="fasta" from_work_dir="out.align1" label="tracy decompose allele1 on ${on_string}" />
48 <data name="out_fasta2" format="fasta" from_work_dir="out.align2" label="tracy decompose allele2 on ${on_string}" />
49 <data name="out_fasta3" format="fasta" from_work_dir="out.align3" label="tracy decompose both alleles on ${on_string}" />
50 <expand macro="tabular_output" toolname="decompose" />
51 <data name="out_bcf" format="bcf" from_work_dir="out.bcf" label="tracy decompose variants on ${on_string}">
52 <filter>callVariants</filter>
53 </data>
54 </outputs>
55 <tests>
56 <test expect_num_outputs="3">
57 <param name="genome" value="reference1.fasta" ftype="fasta" />
58 <param name="tracefile" value="input1.ab1" ftype="ab1" />
59 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
60 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
61 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
62 </test>
63 <test expect_num_outputs="4">
64 <param name="genome" value="reference1.fasta" ftype="fasta" />
65 <param name="tracefile" value="input1.ab1" ftype="ab1" />
66 <param name="callVariants" value="true" />
67 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
68 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
69 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
70 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
71 </test>
72 <test expect_num_outputs="5">
73 <param name="genome" value="reference1.fasta" ftype="fasta" />
74 <param name="tracefile" value="input1.ab1" ftype="ab1" />
75 <param name="callVariants" value="true" />
76 <param name="optional_outputs" value="json" />
77 <output name="out_json" ftype="json">
78 <assert_contents>
79 <has_text text='"peakA": [5, 5, 5, 5, 5, 4' />
80 </assert_contents>
81 </output>
82 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
83 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
84 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
85 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
86 </test>
87 <test expect_num_outputs="5">
88 <param name="genome" value="reference1.fasta" ftype="fasta" />
89 <param name="tracefile" value="input1.ab1" ftype="ab1" />
90 <param name="callVariants" value="true" />
91 <param name="optional_outputs" value="tabular" />
92 <output name="out_stats" ftype="tabular">
93 <assert_contents>
94 <has_text_matching expression="13\s1\s2\s2\s11\s2\sT\sG\sN\s5\sY" />
95 </assert_contents>
96 </output>
97 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
98 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
99 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
100 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
101 </test>
102 </tests>
103 <help><![CDATA[
104 **What this does**
105
106 Double-peaks in a trace file can cause alignment issues. This tool uses tracy_ to decompose
107 heterozygous variants in a trace file into two separate alleles. Each allele is then aligned
108 separately to the reference sequence.
109
110 Optionally, variants between the trace file and the reference are also output in BCF format.
111
112 @pratio@
113
114 @trim_options@
115
116 @alignment@
117
118 Read more here_.
119
120 .. _tracy: https://github.com/gear-genomics/tracy
121 .. _here: https://www.gear-genomics.com/docs/tracy/cli/#deconvolution-of-heterozygous-mutations
122 ]]></help>
123 <expand macro="citations" />
124 </tool>