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comparison tracy_align.xml @ 0:80e3f678b947 draft default tip

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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 14:20:14 +0000
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-1:000000000000 0:80e3f678b947
1 <tool id="tracy_align" name="tracy Align" version="@TOOL_VERSION@+galaxy0" profile="20.09">
2 <description>chromatogram to a FASTA reference</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 $index_genome == True
10 bgzip -c '$reference' > genome.fasta.gz ;
11 tracy index -o genome.fasta.fm9 genome.fasta.gz &&
12 #set refgenome = "genome.fasta.gz"
13 #else
14 #set refgenome = $reference
15 #end if
16 tracy align
17 --reference '$refgenome'
18 --pratio $pratio
19 --kmer $kmer.kmer
20 --support $kmer.support
21 --maxindel $maxindel
22 --trim $trim.trim
23 --trimLeft $trim.trimLeft
24 --trimRight $trim.trimRight
25 --linelimit $linelimit
26 --gapopen $alignment.gapopen
27 --gapext $alignment.gapext
28 --match $alignment.match
29 --mismatch $alignment.mismatch
30 '$tracefile'
31 ]]></command>
32 <inputs>
33 <param argument="--reference" type="data" format="fasta,ab1,scf" label="FASTA, ABI or SCF format reference" />
34 <param name="tracefile" type="data" format="ab1,scf" label="Sanger chromatogram tracefile to align" />
35 <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" />
36 <expand macro="common_options" />
37 <expand macro="kmer_options" />
38 <expand macro="alignment_options" />
39 <expand macro="trim_options" />
40 <expand macro="optional_outputs" />
41 </inputs>
42 <outputs>
43 <expand macro="json_output" toolname="align" />
44 <data name="out_report" format="txt" from_work_dir="out.txt" label="tracy align report on ${on_string}" />
45 <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy align aligned FASTA on ${on_string}" />
46 <expand macro="tabular_output" toolname="align" />
47 </outputs>
48 <tests>
49 <test expect_num_outputs="2">
50 <param name="reference" value="reference1.fasta" ftype="fasta" />
51 <param name="index_genome" value="false" />
52 <param name="tracefile" value="input1.ab1" ftype="ab1" />
53 <output name="out_report" value="out1.txt" ftype="txt" />
54 <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" />
55 </test>
56 <test expect_num_outputs="2">
57 <param name="reference" value="reference1.fasta" ftype="fasta" />
58 <param name="index_genome" value="true" />
59 <param name="tracefile" value="input1.ab1" ftype="ab1" />
60 <output name="out_report" value="out2.txt" ftype="txt" />
61 <output name="out_alignment" value="out2.fasta" ftype="fasta" lines_diff="2" />
62 </test>
63 <test expect_num_outputs="4">
64 <param name="reference" value="reference1.fasta" ftype="fasta" />
65 <param name="index_genome" value="false" />
66 <param name="tracefile" value="input1.ab1" ftype="ab1" />
67 <param name="optional_outputs" value="json,tabular" />
68 <output name="out_report" value="out1.txt" ftype="txt" />
69 <output name="out_json" ftype="json">
70 <assert_contents>
71 <has_text text='"peakA": [5, 5, 5, 5, 5, 4' />
72 </assert_contents>
73 </output>
74 <output name="out_stats" ftype="tabular">
75 <assert_contents>
76 <has_text_matching expression="13\s1\s2\s2\s11\s2\sT\sG\sN\s5\sY" />
77 </assert_contents>
78 </output>
79 <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" />
80 </test>
81
82 </tests>
83 <help><![CDATA[
84 **What it does**.
85
86 Align a chromatogram trace to a reference nucleotide sequence (using tracy_). The reference can either be a FASTA file
87 or a trace file.
88
89 For genomes larger than 50 kilobases, the genome should be indexed before alignment. Indexed genomes use a FM index to find
90 matching kmers to anchor the dynamic programming search for an alignment.
91
92 **NOTE** tracy_ cannot align traces that overlap the ends of a circular genome correctly.
93
94 @pratio@
95
96 @trim_options@
97
98 @alignment@
99
100 Read more here_.
101
102 .. _tracy: https://github.com/gear-genomics/tracy
103 .. _here: https://www.gear-genomics.com/docs/tracy/cli/#trace-alignment
104 ]]></help>
105 <expand macro="citations" />
106 </tool>