Mercurial > repos > iuc > tracy_assemble

annotate tracy_assemble.xml @ 0:99d31ec6629b 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 14:20:41 +0000
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99d31ec6629b "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_assemble" name="tracy Assemble" version="@TOOL_VERSION@+galaxy0" profile="20.09">
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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2 <description>genomic region from tiled, overlapping Sanger Chromatogram trace files</description>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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3 <macros>
99d31ec6629b "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>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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5 </macros>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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6 <expand macro="requirements" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
iuc
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7 <expand macro="version_command" />
99d31ec6629b "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[
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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9 tracy assemble
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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10 #if $ref.useref == 'yes':
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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11 --reference '$ref.reference'
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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12 $ref.incref
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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13 #end if
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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14 --pratio $pratio
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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15 --trim $trim
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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16 --fracmatch $fracmatch
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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17 --called $called
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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18 --format $format
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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19 $inccons
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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20 --gapopen $alignment.gapopen
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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21 --gapext $alignment.gapext
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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22 --match $alignment.match
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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23 --mismatch $alignment.mismatch
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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24 #for tracefile in $tracefiles
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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25 '$tracefile'
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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26 #end for
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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27 &&
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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28 #if $format == 'fastq'
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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29 mv out.cons.fq '$out_consensus'
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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30 #else
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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31 mv out.cons.fa '$out_consensus'
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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32 #end if
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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33 ]]></command>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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34 <inputs>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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35 <param name="tracefiles" type="data" format="ab1,scf" multiple="true" optional="false" label="Sanger chromatogram tracefiles to assemble" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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36 <param argument="--pratio" type="float" value="0.33" label="Peak ratio to call base" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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37 <param argument="--trim" type="integer" value="4" min="1" label="Trimming stringency" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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38 <param argument="--fracmatch" type="float" value="0.5" min="0" max="1" label="Minimum fraction of matches [0:1]" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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39 <param argument="--called" type="float" value="0.1" min="0" label="Fraction of traces required for consensus" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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40 <param argument="--format" type="select" label="Output format">
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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41 <option value="fasta" selected="true">FASTA</option>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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42 <option value="fastq">FASTQ</option>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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43 </param>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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44 <param argument="--inccons" type="boolean" truevalue="--inccons" falsevalue="" label="Include consensus in FASTA alignment" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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45 <conditional name="ref" label="Reference guided assembly options">
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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46 <param type="select" name="useref" label="Use reference to guide assembly">
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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47 <option value="yes">Yes</option>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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48 <option value="no" selected="true">No</option>
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49 </param>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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50 <when value="yes">
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51 <param argument="--reference" type="data" format="fasta" label="FASTA or ABI format genome" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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52 <param argument="--incref" type="boolean" truevalue="--incref" falsevalue="" label="Include reference in consensus" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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53 </when>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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54 <when value="no">
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55 </when>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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56 </conditional>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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57 <expand macro="alignment_options" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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58 <param name="json_output" type="boolean" label="Produce JSON output" />
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59 </inputs>
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60 <outputs>
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61 <data name="out_json" format="json" from_work_dir="out.json" label="tracy assemble JSON on ${on_string}">
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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62 <filter>json_output</filter>
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63 </data>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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64 <data name="out_consensus" format="fasta" label="tracy assemble consensus on ${on_string}">
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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65 <change_format>
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66 <when input="format" value="fasta" format="fasta" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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67 <when input="format" value="fastq" format="fastq" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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68 </change_format>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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69 </data>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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70 <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy assemble alignment on ${on_string}" />
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71 </outputs>
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72 <tests>
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73 <test expect_num_outputs="2">
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74 <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" />
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75 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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76 <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" />
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77 </test>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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78 <test expect_num_outputs="2">
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79 <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" />
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80 <conditional name="ref">
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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81 <param name="useref" value="yes" />
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82 <param name="reference" value="reference1.fasta" />
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83 </conditional>
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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84 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />
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85 <output name="out_alignment" value="out2.alignment.fasta" ftype="fasta" lines_diff="4" />
99d31ec6629b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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86 </test>
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87 <test expect_num_outputs="3">
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88 <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" />
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89 <param name="json_output" value="true" />
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90 <output name="out_json" ftype="json">
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91 <assert_contents>
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92 <has_text text='"peakA": [5, 5, 5, 5, 5, 4' />
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93 </assert_contents>
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94 </output>
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95 <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />
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96 <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" />
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97 </test>
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98 </tests>
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99 <help><![CDATA[
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100 **What this does**
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101
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102 This tool assembles trace files that are from overlapping regions (using tracy_), optionally using a reference genome.
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103 The assembled sequence is output either as FASTQ or FASTA.
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104
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105 @pratio@
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106
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107 Prior to assembling the traces, they are trimmed using an algorithm that automatically finds left and right trimming
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108 positions. This algorithm can be tuned using the *trimming stringency* (higher values mean stricter trimmer).
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109
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110 Trace files have to match (either each other or, when using reference guided assembly, the reference sequence)
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111 at at least *fracmatch* positions (by default 10%) to be considered as part of the assembly.
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112
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113 Read more here_.
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114
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115 .. _tracy: https://github.com/gear-genomics/tracy
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116 .. _here: https://www.gear-genomics.com/docs/tracy/cli/#trace-assembly
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117
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118 ]]></help>
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119 <expand macro="citations" />
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120 </tool>