Mercurial > repos > iuc > tracy_decompose

annotate tracy_decompose.xml @ 0:6ec40b104f9d 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 14:21:06 +0000
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6ec40b104f9d "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_decompose" name="tracy Decompose" version="@TOOL_VERSION@+galaxy0" profile="20.09">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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2 <description>heterozygous mutations (and call variants)</description>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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3 <macros>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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4 <import>macros.xml</import>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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5 </macros>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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6 <expand macro="requirements" />
6ec40b104f9d "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" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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9 #if $index_genome == True
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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10 bgzip -c '$genome' > genome.fasta.gz ;
6ec40b104f9d "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 &&
6ec40b104f9d "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"
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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13 #else
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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14 #set refgenome = $genome
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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15 #end if
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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16 tracy decompose
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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17 --genome '$refgenome'
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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18 $callVariants
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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19 --pratio $pratio
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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20 --kmer $kmer.kmer
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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21 --support $kmer.support
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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22 --maxindel $maxindel
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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23 --trim $trim.trim
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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24 --trimLeft $trim.trimLeft
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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25 --trimRight $trim.trimRight
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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26 --linelimit $linelimit
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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27 --gapopen $alignment.gapopen
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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28 --gapext $alignment.gapext
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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29 --match $alignment.match
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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30 --mismatch $alignment.mismatch
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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31 '$tracefile'
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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32 ]]></command>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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33 <inputs>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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34 <param argument="--genome" type="data" format="fasta,ab1,scf" label="FASTA, ABI or SCF format genome" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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35 <param name="tracefile" type="data" format="ab1,scf" label="Sanger chromatogram tracefile to align" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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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" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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37 <param argument="--callVariants" type="boolean" truevalue="--callVariants" falsevalue="" label="Call variants in chromatogram" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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38 <!-- annotate option is not yet supported -->
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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39 <expand macro="common_options" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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40 <expand macro="kmer_options" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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41 <expand macro="alignment_options" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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42 <expand macro="trim_options" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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43 <expand macro="optional_outputs" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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44 </inputs>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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45 <outputs>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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46 <expand macro="json_output" toolname="decompose" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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47 <data name="out_fasta1" format="fasta" from_work_dir="out.align1" label="tracy decompose allele1 on ${on_string}" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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48 <data name="out_fasta2" format="fasta" from_work_dir="out.align2" label="tracy decompose allele2 on ${on_string}" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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49 <data name="out_fasta3" format="fasta" from_work_dir="out.align3" label="tracy decompose both alleles on ${on_string}" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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50 <expand macro="tabular_output" toolname="decompose" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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51 <data name="out_bcf" format="bcf" from_work_dir="out.bcf" label="tracy decompose variants on ${on_string}">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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52 <filter>callVariants</filter>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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53 </data>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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54 </outputs>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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55 <tests>
6ec40b104f9d "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="3">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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57 <param name="genome" value="reference1.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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58 <param name="tracefile" value="input1.ab1" ftype="ab1" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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59 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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60 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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61 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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62 </test>
6ec40b104f9d "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">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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64 <param name="genome" value="reference1.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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65 <param name="tracefile" value="input1.ab1" ftype="ab1" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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66 <param name="callVariants" value="true" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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67 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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68 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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69 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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70 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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71 </test>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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72 <test expect_num_outputs="5">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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73 <param name="genome" value="reference1.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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74 <param name="tracefile" value="input1.ab1" ftype="ab1" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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75 <param name="callVariants" value="true" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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76 <param name="optional_outputs" value="json" />
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77 <output name="out_json" ftype="json">
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78 <assert_contents>
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79 <has_text text='"peakA": [5, 5, 5, 5, 5, 4' />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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80 </assert_contents>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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81 </output>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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82 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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83 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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84 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
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85 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
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86 </test>
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87 <test expect_num_outputs="5">
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88 <param name="genome" value="reference1.fasta" ftype="fasta" />
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89 <param name="tracefile" value="input1.ab1" ftype="ab1" />
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90 <param name="callVariants" value="true" />
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91 <param name="optional_outputs" value="tabular" />
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92 <output name="out_stats" ftype="tabular">
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93 <assert_contents>
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94 <has_text_matching expression="13\s1\s2\s2\s11\s2\sT\sG\sN\s5\sY" />
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95 </assert_contents>
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96 </output>
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97 <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" />
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98 <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" />
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99 <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" />
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100 <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" />
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101 </test>
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102 </tests>
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103 <help><![CDATA[
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104 **What this does**
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105
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106 Double-peaks in a trace file can cause alignment issues. This tool uses tracy_ to decompose
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107 heterozygous variants in a trace file into two separate alleles. Each allele is then aligned
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108 separately to the reference sequence.
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109
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110 Optionally, variants between the trace file and the reference are also output in BCF format.
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111
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112 @pratio@
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113
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114 @trim_options@
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115
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116 @alignment@
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117
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118 Read more here_.
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119
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120 .. _tracy: https://github.com/gear-genomics/tracy
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121 .. _here: https://www.gear-genomics.com/docs/tracy/cli/#deconvolution-of-heterozygous-mutations
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122 ]]></help>
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123 <expand macro="citations" />
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124 </tool>