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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
author jvolkening
date Wed, 06 Mar 2024 06:40:22 +0000
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0
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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1 <tool id="badread" name="Badread" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="MIT" python_template_version="3.5" profile="21.05">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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2
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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3 <description>long-read simulator</description>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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4 <macros>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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5 <token name="@TOOL_VERSION@">0.4.1</token>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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6 <token name="@VERSION_SUFFIX@">0</token>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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7 </macros>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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8 <edam_topics>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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9 <edam_topic>topic_0080</edam_topic> <!-- Sequence analysis -->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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10 </edam_topics>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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11 <edam_operations>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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12 <edam_operation>operation_2426</edam_operation> <!-- Modelling and simulation -->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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13 </edam_operations>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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14 <requirements>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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15 <requirement type="package" version="@TOOL_VERSION@">badread</requirement>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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16 <requirement type="package" version="2.8">pigz</requirement>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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17 </requirements>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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18 <version_command>badread --version | perl -wpe 's/Badread v//'</version_command>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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19
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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20 <command detect_errors="aggressive"><![CDATA[
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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21 badread simulate
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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22 --reference '${io.reference}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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23 --quantity '${sim.quantity}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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24 --length '${sim.length}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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25 --identity '${sim.identity}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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26 --error_model '${sim.error_model}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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27 --qscore_model '${sim.qscore_model}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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28 #if str($sim.seed.seed_bool) == "True":
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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29 --seed ${sim.seed.seed}
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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30 #end if
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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31 --start_adapter '${adapt.start_adapter}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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32 --end_adapter '${adapt.end_adapter}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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33 --start_adapter_seq '${adapt.start_adapter_seq}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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34 --end_adapter_seq '${adapt.end_adapter_seq}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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35 --junk_reads ${problems.junk_reads}
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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36 --random_reads ${problems.random_reads}
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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37 --chimera ${problems.chimera}
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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38 --glitches '${problems.glitches}'
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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39 $small_plasmid_bias
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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40 ${io.compress_output}
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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41 > $output
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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42 ]]></command>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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43
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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44 <inputs>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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45 <section name="io" title="Input/Output" expanded="true">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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46 <param type="data"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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47 argument="--reference"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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48 format="fasta,fasta.gz"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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49 label="Reference"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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50 help="Reference file in FASTA format"/>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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51 <param type="boolean"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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52 name="compress_output"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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53 checked="true"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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54 truevalue="| pigz -p ${GALAXY_SLOTS:-1} --no-name --no-time"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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55 falsevalue=""
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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56 label="Compress output" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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57 </section>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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58 <section name="sim" title="Simulation parameters" expanded="true">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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59 <param type="text"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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60 optional="false"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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61 argument="--quantity"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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62 label="Quantity"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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63 help="Absolute number of bp (e.g. '250M') or relative depth (e.g. '25x')">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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64 <validator type="regex">^\d+(?i:[xkmg])?$</validator>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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65 <validator type="empty_field" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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66 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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67 <param type="text"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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68 argument="--length"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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69 value="15000,13000"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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70 label="Fragment length distribution"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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71 help="'mean,stdev'">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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72 <validator type="regex">^\d+,\d+$</validator>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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73 </param>
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74 <param type="text"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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75 argument="--identity"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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76 value="95,99,2.5"
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77 label="Identity distribution"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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78 help="'mean,max,stdev' for identity beta distribution, 'mean,stdev' for qscore normal distribution">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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79 <validator type="regex">^[\d\.]+,[\d\.]+(,[\d\.]+)?$</validator>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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80 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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81 <param type="select" argument="--error_model" label="Error model">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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82 <option value="nanopore2018">nanopore2018</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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83 <option value="nanopore2020">nanopore2020</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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84 <option value="nanopore2023" selected="true">nanopore2023</option>
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85 <option value="pacbio2016">pacbio2016</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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86 <option value="pacbio2021">pacbio2021</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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87 <option value="random">random</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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88 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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89 <param type="select" argument="--qscore_model" label="Q-score model">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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90 <option value="nanopore2018">nanopore2018</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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91 <option value="nanopore2020">nanopore2020</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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92 <option value="nanopore2023" selected="true">nanopore2023</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
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93 <option value="pacbio2016">pacbio2016</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
94 <option value="pacbio2021">pacbio2021</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
95 <option value="random">random</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
96 <option value="ideal">ideal</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
97 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
98 <conditional name="seed">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
99 <param name="seed_bool" type="select" label="Fixed seed?">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
100 <option value="False" selected="true">No</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
101 <option value="True">Yes</option>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
102 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
103 <when value="True">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
104 <param argument="--seed" type="integer" value="1234" label="Enter seed" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
105 </when>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
106 <when value="False" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
107 </conditional>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
108 </section>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
109 <section name="adapt" title="Adapters">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
110 <param type="text"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
111 argument="--start_adapter"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
112 value="90,60"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
113 label="Start adapter"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
114 help="'rate,amount'">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
115 <validator type="regex">^\d+,\d+$</validator>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
116 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
117 <param type="text"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
118 argument="--end_adapter"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
119 value="50,20"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
120 label="End adapter"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
121 help="'rate,amount'">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
122 <validator type="regex">^\d+,\d+$</validator>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
123 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
124 <param type="text"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
125 argument="--start_adapter_seq"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
126 value="AATGTACTTCGTTCAGTTACGTATTGCT"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
127 label="Start adapter sequence">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
128 <validator type="regex">^(?i:[ATGC]+)$</validator>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
129 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
130 <param type="text"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
131 argument="--end_adapter_seq"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
132 value="GCAATACGTAACTGAACGAAGT"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
133 label="End adapter sequence">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
134 <validator type="regex">^(?i:[ATGC]+)$</validator>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
135 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
136 </section>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
137 <section name="problems" title="Problems">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
138 <param type="float"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
139 argument="--junk_reads"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
140 value="1"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
141 min="0"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
142 max="100"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
143 label="Percentage junk reads"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
144 help="0-100" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
145 <param type="float"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
146 argument="--random_reads"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
147 value="1"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
148 min="0"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
149 max="100"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
150 label="Percentage random reads"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
151 help="0-100" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
152 <param type="float"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
153 argument="--chimera"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
154 value="1"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
155 min="0"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
156 max="50"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
157 label="Percentage chimeric formation"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
158 help="0-50" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
159 <param type="text"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
160 argument="--glitches"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
161 value="10000,25,25"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
162 label="Read glitches"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
163 help="'rate,size,skip'">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
164 <validator type="regex">^\d+,\d+,\d+$</validator>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
165 </param>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
166 <param type="boolean"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
167 argument="--small_plasmid_bias"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
168 checked="false"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
169 truevalue="--small_plasmid_bias"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
170 falsevalue=""
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
171 label="Small plasmid bias"
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
172 help="Drop circular sequences smaller than fragment length" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
173 </section>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
174 </inputs>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
175
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
176 <outputs>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
177 <data name="output" format="fastq.gz">
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
178 <change_format>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
179 <when input="io.compress_output" value="" format="fastq" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
180 </change_format>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
181 </data>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
182 </outputs>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
183
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
184 <tests>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
185 <!-- defaults with seed -->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
186 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
187 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
188 <param name="seed_bool" value="True" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
189 <param name="seed" value="22" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
190 <param name="quantity" value="2x" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
191 <output name="output" file="2x.fq.gz" compare="diff" ftype="fastq.gz" decompress="true" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
192 <assert_command>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
193 <has_text text="--seed 22" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
194 </assert_command>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
195 </test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
196 <!-- defaults without seed -->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
197 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
198 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
199 <param name="quantity" value="2x" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
200 <assert_command>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
201 <not_has_text text="--seed " />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
202 </assert_command>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
203 </test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
204 <!-- use absolute quanitity w/o compression-->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
205 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
206 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
207 <param name="seed_bool" value="True" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
208 <param name="seed" value="22" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
209 <param name="quantity" value="50k" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
210 <param name="compress_output" value="false" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
211 <output name="output" file="50k.fq.gz" compare="diff" ftype="fastq" decompress="true" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
212 </test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
213 <!-- set length dist-->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
214 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
215 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
216 <param name="seed_bool" value="True" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
217 <param name="seed" value="22" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
218 <param name="quantity" value="2x" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
219 <param name="length" value="2000,1000" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
220 <output name="output" file="2x.l2000_1000.fq.gz" compare="diff" decompress="true" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
221 </test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
222 <!-- set identity as beta dist-->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
223 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
224 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
225 <param name="seed_bool" value="True" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
226 <param name="seed" value="22" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
227 <param name="quantity" value="2x" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
228 <param name="identity" value="80,90,5" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
229 <output name="output" file="2x.i80_90_5.fq.gz" compare="diff" decompress="true" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
230 <assert_stderr>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
231 <has_text text="identities from a beta distribution" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
232 </assert_stderr>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
233 </test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
234 <!-- set identity as normal dist-->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
235 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
236 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
237 <param name="seed_bool" value="True" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
238 <param name="seed" value="22" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
239 <param name="quantity" value="2x" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
240 <param name="identity" value="80,5" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
241 <output name="output" file="2x.i80_5.fq.gz" compare="diff" decompress="true" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
242 <assert_stderr>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
243 <has_text text="qscores from a normal distribution" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
244 </assert_stderr>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
245 </test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
246 <!-- other models -->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
247 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
248 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
249 <param name="seed_bool" value="True" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
250 <param name="seed" value="22" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
251 <param name="quantity" value="2x" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
252 <param name="error_model" value="pacbio2021" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
253 <param name="qscore_model" value="pacbio2021" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
254 <output name="output" file="2x.em_pacbio2021.qm_pacbio2021.fq.gz" compare="diff" decompress="true" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
255 </test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
256 <!-- set non-default adapters-->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
257 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
258 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
259 <param name="seed_bool" value="True" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
260 <param name="seed" value="22" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
261 <param name="quantity" value="2x" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
262 <param name="start_adapter" value="50,30" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
263 <param name="start_adapter_seq" value="ATGC" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
264 <param name="end_adapter" value="80,40" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
265 <param name="end_adapter_seq" value="GCAT" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
266 <output name="output" file="2x.sa50_30_ATGC.ea80_40_GCAT.fq.gz" compare="diff" decompress="true" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
267 </test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
268 <!-- set problem parameters-->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
269 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
270 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
271 <param name="seed_bool" value="True" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
272 <param name="seed" value="22" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
273 <param name="quantity" value="2x" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
274 <param name="junk_reads" value="80" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
275 <param name="random_reads" value="9.5" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
276 <param name="chimera" value="5" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
277 <param name="glitches" value="2000,50,40" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
278 <output name="output" file="2x.j80.r9.5.c5.g2000_50_40.fq.gz" compare="diff" decompress="true" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
279 </test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
280 <!-- without and with small plasmid bias-->
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
281 <test>
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
282 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
diff changeset
283 <param name="seed_bool" value="True" />
050e560dd49f planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/badread commit fa7861da52408457fa440bf5efe45963f333f282
jvolkening
parents:
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284 <param name="seed" value="22" />
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285 <param name="quantity" value="1M" />
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286 <output name="output" decompress="true">
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287 <assert_contents>
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288 <has_text text="GU320569" />
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289 </assert_contents>
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290 </output>
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291 </test>
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292 <test>
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293 <param name="reference" value="ref.fa.gz" ftype="fasta.gz" />
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294 <param name="seed_bool" value="True" />
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295 <param name="seed" value="22" />
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296 <param name="quantity" value="1M" />
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297 <param name="small_plasmid_bias" value="true" />
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298 <output name="output" decompress="true">
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299 <assert_contents>
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300 <not_has_text text="GU320569" />
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301 </assert_contents>
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302 </output>
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303 </test>
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304 </tests>
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305
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306 <help><![CDATA[
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307 **Required arguments:**
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308
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309 --reference REFERENCE Reference FASTA file (can be gzipped)
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310 --quantity QUANTITY Either an absolute value (e.g. 250M) or a
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311 relative depth (e.g. 25x)
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312
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313 **Simulation parameters:**
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314
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315 --length LENGTH Fragment length distribution (mean and stdev,
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316 default: 15000,13000)
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317 --identity IDENTITY Sequencing identity distribution
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318 (mean,max,stdev for beta distribution or
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319 mean,stdev for normal qscore distribution,
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320 default: 95,99,2.5)
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321 --error_model ERROR_MODEL Can be "nanopore2018", "nanopore2020",
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322 "nanopore2023", "pacbio2016", "pacbio2021",
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323 "random" or a model filename (default:
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324 nanopore2023)
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325 --qscore_model QSCORE_MODEL Can be "nanopore2018", "nanopore2020",
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326 "nanopore2023", "pacbio2016", "pacbio2021",
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327 "random", "ideal" or a model filename
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328 (default: nanopore2023)
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329 --seed SEED Random number generator seed for deterministic
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330 output (default: different output each time)
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331
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332 **Adapters:**
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333
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334 --start_adapter START_ADAPTER
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335 Adapter parameters for read starts (rate and
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336 amount, default: 90,60)
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337 --end_adapter END_ADAPTER Adapter parameters for read ends (rate and
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338 amount, default: 50,20)
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339 --start_adapter_seq START_ADAPTER_SEQ
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340 Adapter sequence for read starts (default:
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341 AATGTACTTCGTTCAGTTACGTATTGCT)
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342 --end_adapter_seq END_ADAPTER_SEQ
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343 Adapter sequence for read ends (default:
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344 GCAATACGTAACTGAACGAAGT)
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345
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346 **Problems:**
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347
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348 --junk_reads JUNK_READS This percentage of reads will be
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349 low-complexity junk (default: 1)
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350 --random_reads RANDOM_READS This percentage of reads will be random
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351 sequence (default: 1)
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352 --chimeras CHIMERAS Percentage at which separate fragments join
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353 together (default: 1)
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354 --glitches GLITCHES Read glitch parameters (rate, size and skip,
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355 default: 10000,25,25)
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356 --small_plasmid_bias If set, then small circular plasmids are lost
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357 when the fragment length is too high (default:
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358 small plasmids are included regardless of
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359 fragment length)
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360
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361 ]]></help>
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362
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363 <citations>
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364 <citation type="doi">10.21105/joss.01316</citation>
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365 </citations>
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366
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367 </tool>