Mercurial > repos > iuc > tracy_align

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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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80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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1 <tool id="tracy_align" name="tracy Align" version="@TOOL_VERSION@+galaxy0" profile="20.09">
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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2 <description>chromatogram to a FASTA reference</description>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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3 <macros>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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4 <import>macros.xml</import>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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5 </macros>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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6 <expand macro="requirements" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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7 <expand macro="version_command" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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8 <command detect_errors="exit_code"><![CDATA[
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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9 #if $index_genome == True
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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10 bgzip -c '$reference' > genome.fasta.gz ;
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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11 tracy index -o genome.fasta.fm9 genome.fasta.gz &&
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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12 #set refgenome = "genome.fasta.gz"
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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13 #else
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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14 #set refgenome = $reference
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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15 #end if
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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16 tracy align
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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17 --reference '$refgenome'
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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18 --pratio $pratio
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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19 --kmer $kmer.kmer
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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20 --support $kmer.support
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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21 --maxindel $maxindel
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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22 --trim $trim.trim
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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23 --trimLeft $trim.trimLeft
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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24 --trimRight $trim.trimRight
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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25 --linelimit $linelimit
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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26 --gapopen $alignment.gapopen
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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27 --gapext $alignment.gapext
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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28 --match $alignment.match
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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29 --mismatch $alignment.mismatch
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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30 '$tracefile'
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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31 ]]></command>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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32 <inputs>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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33 <param argument="--reference" type="data" format="fasta,ab1,scf" label="FASTA, ABI or SCF format reference" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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34 <param name="tracefile" type="data" format="ab1,scf" label="Sanger chromatogram tracefile to align" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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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" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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36 <expand macro="common_options" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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37 <expand macro="kmer_options" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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38 <expand macro="alignment_options" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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39 <expand macro="trim_options" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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40 <expand macro="optional_outputs" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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41 </inputs>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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42 <outputs>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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43 <expand macro="json_output" toolname="align" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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44 <data name="out_report" format="txt" from_work_dir="out.txt" label="tracy align report on ${on_string}" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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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}" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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46 <expand macro="tabular_output" toolname="align" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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47 </outputs>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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48 <tests>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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49 <test expect_num_outputs="2">
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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50 <param name="reference" value="reference1.fasta" ftype="fasta" />
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51 <param name="index_genome" value="false" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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52 <param name="tracefile" value="input1.ab1" ftype="ab1" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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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" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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55 </test>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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56 <test expect_num_outputs="2">
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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57 <param name="reference" value="reference1.fasta" ftype="fasta" />
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58 <param name="index_genome" value="true" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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59 <param name="tracefile" value="input1.ab1" ftype="ab1" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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60 <output name="out_report" value="out2.txt" ftype="txt" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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61 <output name="out_alignment" value="out2.fasta" ftype="fasta" lines_diff="2" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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62 </test>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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63 <test expect_num_outputs="4">
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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64 <param name="reference" value="reference1.fasta" ftype="fasta" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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65 <param name="index_genome" value="false" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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66 <param name="tracefile" value="input1.ab1" ftype="ab1" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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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" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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69 <output name="out_json" ftype="json">
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70 <assert_contents>
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71 <has_text text='"peakA": [5, 5, 5, 5, 5, 4' />
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72 </assert_contents>
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73 </output>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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74 <output name="out_stats" ftype="tabular">
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75 <assert_contents>
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76 <has_text_matching expression="13\s1\s2\s2\s11\s2\sT\sG\sN\s5\sY" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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77 </assert_contents>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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78 </output>
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79 <output name="out_alignment" value="out1.fasta" ftype="fasta" lines_diff="2" />
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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80 </test>
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81
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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82 </tests>
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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83 <help><![CDATA[
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84 **What it does**.
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85
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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86 Align a chromatogram trace to a reference nucleotide sequence (using tracy_). The reference can either be a FASTA file
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87 or a trace file.
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88
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89 For genomes larger than 50 kilobases, the genome should be indexed before alignment. Indexed genomes use a FM index to find
80e3f678b947 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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90 matching kmers to anchor the dynamic programming search for an alignment.
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91
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92 **NOTE** tracy_ cannot align traces that overlap the ends of a circular genome correctly.
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93
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94 @pratio@
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95
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96 @trim_options@
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97
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98 @alignment@
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99
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100 Read more here_.
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101
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102 .. _tracy: https://github.com/gear-genomics/tracy
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103 .. _here: https://www.gear-genomics.com/docs/tracy/cli/#trace-alignment
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104 ]]></help>
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105 <expand macro="citations" />
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106 </tool>