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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"
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1 <macros>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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2 <token name="@TOOL_VERSION@">0.6.1</token>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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3 <xml name="requirements">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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4 <requirements>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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5 <requirement type="package" version="@TOOL_VERSION@">tracy</requirement>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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6 <yield/>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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7 </requirements>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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8 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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9 <xml name="citations">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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10 <citations>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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11 <citation type="doi">10.1186/s12864-020-6635-8</citation>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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12 <yield />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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13 </citations>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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14 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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15 <xml name="version_command">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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16 <version_command>tracy --version</version_command>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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17 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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18 <xml name="common_options">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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19 <param argument="--pratio" type="float" value="0.33" label="Peak ratio to call base" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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20 <param argument="--maxindel" type="integer" value="1000" label="Maximum indel size in Sanger trace" min="1" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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21 <param argument="--linelimit" type="integer" value="60" label="Alignment line length" min="1" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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22 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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23 <xml name="kmer_options">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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24 <section name="kmer" title="Kmer options">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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25 <param argument="--kmer" type="integer" value="15" label="Kmer size to anchor trace" min="1" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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26 <param argument="--support" type="integer" value="3" label="Minimum kmer support" min="1" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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27 </section>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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28 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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29 <xml name="trim_options">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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30 <section name="trim" title="Trimming options">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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31 <param argument="--trim" type="integer" value="0" label="Trimming stringency (0: use trimLeft and trimRight)" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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32 <param argument="--trimLeft" type="integer" value="50" label="Trim size left" min="0" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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33 <param argument="--trimRight" type="integer" value="50" label="Trim size right" min="0" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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34 </section>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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35 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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36 <xml name="alignment_options">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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37 <section name="alignment" title="Alignment options">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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38 <param argument="--gapopen" type="integer" value="-10" max="0" label="Gap open penalty" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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39 <param argument="--gapext" type="integer" value="-4" max="0" label="Gap extension penalty" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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40 <param argument="--match" type="integer" value="3" min="0" label="Match score" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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41 <param argument="--mismatch" type="integer" value="-5" max="0" label="Mismatch penalty" />
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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42 </section>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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43 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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44 <token name="@pratio@"><![CDATA[
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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45 The *pratio* parameter is a floating point value expressing the minimum proportion of the maximum trace value that will still be
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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46 called as a base. For example, if the maximum value found in the trace file is 10, and pratio is 0.3, a peak needs to be
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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47 higher than 3 to be called as a base.
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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48 ]]></token>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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49 <token name="@trim_options@"><![CDATA[
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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50 Prior to alignment the trace file is trimmed. Either a fixed number of bases can be trimmed from the left or right sides of
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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51 the trace, or trimming points (on the left or right or the trace) can be automatically found using an algorithm that works
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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52 outwards from the best 10% of the trace and uses a sliding window (of size 10 bases) to find the point where the trace
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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53 quality falls below a computed threshold. This automated trimming algorithm can be tuned using a *trimming stringency* (higher
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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54 values mean stricter trimming).
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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55 ]]></token>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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56 <token name="@alignment@"><![CDATA[
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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57 The dynamic programming step of the alignment uses the `Gotoh's algorithm <http://rna.informatik.uni-freiburg.de/Teaching/index.jsp?toolName=Gotoh>`_
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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58 which can be tuned using scores for nucleotide matches, mismatches, gap opening and gap extension.
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59 ]]></token>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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60 <xml name="optional_outputs">
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61 <param name="optional_outputs" type="select" multiple="true" label="Optional outputs">
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62 <option value="json">JSON</option>
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63 <option value="tabular">tabular statistics report</option>
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64 </param>
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65 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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66 <xml name="json_output" token_toolname="">
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67 <data name="out_json" format="json" from_work_dir="out.json" label="tracy @TOOLNAME@ JSON on ${on_string}">
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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68 <filter>optional_outputs and 'json' in optional_outputs</filter>
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69 </data>
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70 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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71 <xml name="tabular_output" token_toolname="">
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72 <data name="out_stats" format="tabular" from_work_dir="out.abif" label="tracy @TOOLNAME@ stats on ${on_string}">
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73 <actions>
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74 <action name="column_names" type="metadata" default="pos,peakA,peakC,peakG,peakT,basenum,primary,secondary,consensus,qual,trim" />
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75 </actions>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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76 <filter>optional_outputs and 'tabular' in optional_outputs</filter>
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77 </data>
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78 </xml>
6ec40b104f9d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217"
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79 </macros>