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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 14:20:41 +0000
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1 <tool id="tracy_assemble" name="tracy Assemble" version="@TOOL_VERSION@+galaxy0" profile="20.09">
2 <description>genomic region from tiled, overlapping Sanger Chromatogram trace files</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 tracy assemble
10 #if $ref.useref == 'yes':
11 --reference '$ref.reference'
12 $ref.incref
13 #end if
14 --pratio $pratio
15 --trim $trim
16 --fracmatch $fracmatch
17 --called $called
18 --format $format
19 $inccons
20 --gapopen $alignment.gapopen
21 --gapext $alignment.gapext
22 --match $alignment.match
23 --mismatch $alignment.mismatch
24 #for tracefile in $tracefiles
25 '$tracefile'
26 #end for
27 &&
28 #if $format == 'fastq'
29 mv out.cons.fq '$out_consensus'
30 #else
31 mv out.cons.fa '$out_consensus'
32 #end if
33 ]]></command>
34 <inputs>
35 <param name="tracefiles" type="data" format="ab1,scf" multiple="true" optional="false" label="Sanger chromatogram tracefiles to assemble" />
36 <param argument="--pratio" type="float" value="0.33" label="Peak ratio to call base" />
37 <param argument="--trim" type="integer" value="4" min="1" label="Trimming stringency" />
38 <param argument="--fracmatch" type="float" value="0.5" min="0" max="1" label="Minimum fraction of matches [0:1]" />
39 <param argument="--called" type="float" value="0.1" min="0" label="Fraction of traces required for consensus" />
40 <param argument="--format" type="select" label="Output format">
41 <option value="fasta" selected="true">FASTA</option>
42 <option value="fastq">FASTQ</option>
43 </param>
44 <param argument="--inccons" type="boolean" truevalue="--inccons" falsevalue="" label="Include consensus in FASTA alignment" />
45 <conditional name="ref" label="Reference guided assembly options">
46 <param type="select" name="useref" label="Use reference to guide assembly">
47 <option value="yes">Yes</option>
48 <option value="no" selected="true">No</option>
49 </param>
50 <when value="yes">
51 <param argument="--reference" type="data" format="fasta" label="FASTA or ABI format genome" />
52 <param argument="--incref" type="boolean" truevalue="--incref" falsevalue="" label="Include reference in consensus" />
53 </when>
54 <when value="no">
55 </when>
56 </conditional>
57 <expand macro="alignment_options" />
58 <param name="json_output" type="boolean" label="Produce JSON output" />
59 </inputs>
60 <outputs>
61 <data name="out_json" format="json" from_work_dir="out.json" label="tracy assemble JSON on ${on_string}">
62 <filter>json_output</filter>
63 </data>
64 <data name="out_consensus" format="fasta" label="tracy assemble consensus on ${on_string}">
65 <change_format>
66 <when input="format" value="fasta" format="fasta" />
67 <when input="format" value="fastq" format="fastq" />
68 </change_format>
69 </data>
70 <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy assemble alignment on ${on_string}" />
71 </outputs>
72 <tests>
73 <test expect_num_outputs="2">
74 <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" />
75 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />
76 <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" />
77 </test>
78 <test expect_num_outputs="2">
79 <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" />
80 <conditional name="ref">
81 <param name="useref" value="yes" />
82 <param name="reference" value="reference1.fasta" />
83 </conditional>
84 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />
85 <output name="out_alignment" value="out2.alignment.fasta" ftype="fasta" lines_diff="4" />
86 </test>
87 <test expect_num_outputs="3">
88 <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" />
89 <param name="json_output" value="true" />
90 <output name="out_json" ftype="json">
91 <assert_contents>
92 <has_text text='"peakA": [5, 5, 5, 5, 5, 4' />
93 </assert_contents>
94 </output>
95 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />
96 <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" />
97 </test>
98 </tests>
99 <help><![CDATA[
100 **What this does**
101
102 This tool assembles trace files that are from overlapping regions (using tracy_), optionally using a reference genome.
103 The assembled sequence is output either as FASTQ or FASTA.
104
105 @pratio@
106
107 Prior to assembling the traces, they are trimmed using an algorithm that automatically finds left and right trimming
108 positions. This algorithm can be tuned using the *trimming stringency* (higher values mean stricter trimmer).
109
110 Trace files have to match (either each other or, when using reference guided assembly, the reference sequence)
111 at at least *fracmatch* positions (by default 10%) to be considered as part of the assembly.
112
113 Read more here_.
114
115 .. _tracy: https://github.com/gear-genomics/tracy
116 .. _here: https://www.gear-genomics.com/docs/tracy/cli/#trace-assembly
117
118 ]]></help>
119 <expand macro="citations" />
120 </tool>