Mercurial > repos > iuc > tracy_align

annotate tracy_align.xml @ 1:31599dc6380f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8eb3532d394f6a44d1edbcbe5ef05fd0474cdab3
author iuc
date Thu, 20 Mar 2025 07:17:06 +0000
parents 726b73198fdc
children
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1
31599dc6380f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8eb3532d394f6a44d1edbcbe5ef05fd0474cdab3
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1 <tool id="tracy_align" name="tracy Align" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
0
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2 <description>chromatogram to a FASTA reference</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #if $index_genome == True
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10 bgzip -c '$reference' > genome.fasta.gz ;
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11 tracy index -o genome.fasta.fm9 genome.fasta.gz &&
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12 #set refgenome = "genome.fasta.gz"
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13 #else
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14 #set refgenome = $reference
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15 #end if
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16 tracy align
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17 --reference '$refgenome'
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18 --pratio $pratio
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19 --kmer $kmer.kmer
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20 --support $kmer.support
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21 --maxindel $maxindel
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22 --trim $trim.trim
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23 --trimLeft $trim.trimLeft
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24 --trimRight $trim.trimRight
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25 --linelimit $linelimit
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26 --gapopen $alignment.gapopen
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27 --gapext $alignment.gapext
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28 --match $alignment.match
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29 --mismatch $alignment.mismatch
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30 '$tracefile'
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31 ]]></command>
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32 <inputs>
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33 <param argument="--reference" type="data" format="fasta,ab1,scf" label="FASTA, ABI or SCF format reference" />
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34 <param name="tracefile" type="data" format="ab1,scf" label="Sanger chromatogram tracefile to align" />
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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" />
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36 <expand macro="common_options" />
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37 <expand macro="kmer_options" />
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38 <expand macro="alignment_options" />
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39 <expand macro="trim_options" />
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40 <expand macro="optional_outputs" />
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41 </inputs>
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42 <outputs>
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43 <expand macro="json_output" toolname="align" />
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44 <data name="out_report" format="txt" from_work_dir="out.txt" label="tracy align report on ${on_string}" />
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45 <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy align aligned FASTA on ${on_string}" />
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46 <expand macro="tabular_output" toolname="align" />
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47 </outputs>
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48 <tests>
1
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49 <test expect_num_outputs="2"> <!-- test 1 -->
0
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50 <param name="reference" value="reference1.fasta" ftype="fasta" />
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51 <param name="index_genome" value="false" />
1
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52 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
0
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53 <output name="out_report" value="out1.txt" ftype="txt" />
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54 <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" />
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55 </test>
1
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56 <test expect_num_outputs="2"> <!-- test 2 -->
0
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57 <param name="reference" value="reference1.fasta" ftype="fasta" />
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58 <param name="index_genome" value="true" />
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59 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
0
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60 <output name="out_report" value="out2.txt" ftype="txt" />
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61 <output name="out_alignment" value="out2.fasta" ftype="fasta" lines_diff="2" />
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62 </test>
1
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63 <test expect_num_outputs="4"> <!-- test 3 -->
0
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64 <param name="reference" value="reference1.fasta" ftype="fasta" />
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65 <param name="index_genome" value="false" />
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66 <param name="tracefile" value="input1_r.ab1" ftype="ab1" />
0
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67 <param name="optional_outputs" value="json,tabular" />
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68 <output name="out_report" value="out1.txt" ftype="txt" />
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69 <output name="out_json" ftype="json">
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70 <assert_contents>
1
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71 <has_text text='"peakA": [20, 20, 20, 19, 19' />
0
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72 </assert_contents>
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73 </output>
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74 <output name="out_stats" ftype="tabular">
1
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75 <assert_contents>
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76 <has_text_matching expression="8\s20\s4\s14\s37\s1\sT\sR\sN\s0\sY" />
0
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77 </assert_contents>
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78 </output>
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79 <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" />
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80 </test>
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81 </tests>
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82 <help><![CDATA[
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83 **What it does**.
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84
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85 Align a chromatogram trace to a reference nucleotide sequence (using tracy_). The reference can either be a FASTA file
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86 or a trace file.
726b73198fdc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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87
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88 For genomes larger than 50 kilobases, the genome should be indexed before alignment. Indexed genomes use a FM index to find
726b73198fdc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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89 matching kmers to anchor the dynamic programming search for an alignment.
726b73198fdc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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90
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91 **NOTE** tracy_ cannot align traces that overlap the ends of a circular genome correctly.
726b73198fdc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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92
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93 @pratio@
726b73198fdc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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94
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95 @trim_options@
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96
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97 @alignment@
726b73198fdc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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98
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99 Read more here_.
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100
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101 .. _tracy: https://github.com/gear-genomics/tracy
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102 .. _here: https://www.gear-genomics.com/docs/tracy/cli/#trace-alignment
726b73198fdc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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103 ]]></help>
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104 <expand macro="citations" />
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105 </tool>