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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
author galaxy-australia
date Fri, 18 Mar 2022 02:10:52 +0000
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0
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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1 <tool id="pbccs" name="CCS" version="0.1.0" python_template_version="3.5">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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2 <description>Generate accurate consensus sequences from subreads</description>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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3 <macros>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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4 <import>macros.xml</import>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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5 </macros>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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6 <expand macro="requirements"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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7 <expand macro="version_command"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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8 <command detect_errors="exit_code"> <![CDATA[
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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9 mkdir -p ./tmp &&
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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10 cp '$input_file' ./tmp/input.bam &&
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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11 cd ./tmp/ &&
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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12 ccs
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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13 -j 4
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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14 #if $input_filter_options.minLength:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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15 --minLength '$input_filter_options.minLength'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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16 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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17 #if $input_filter_options.maxLength:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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18 --maxLength '$input_filter_options.maxLength'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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19 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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20 #if $input_filter_options.minPasses:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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21 --minPasses '$input_filter_options.minPasses'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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22 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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23 #if $input_filter_options.minIdentity:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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24 --minIdentity '$input_filter_options.minIdentity'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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25 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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26 #if $input_filter_options.zmws:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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27 --zmws '$input_filter_options.zmws'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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28 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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29 #if $model_override_options.modelPath:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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30 --modelPath '$model_override_options.modelPath'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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31 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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32 #if $model_override_options.modelSpec:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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33 --modelSpec '$model_override_options.modelSpec'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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34 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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35 #if $output_filter_options.minPredictedAccuracy:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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36 --minPredictedAccuracy '$output_filter_options.minPredictedAccuracy'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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37 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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38 #if $output_filter_options.minReadScore:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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39 --minReadScore '$output_filter_options.minReadScore'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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40 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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41 #if $output_filter_options.maxDropFraction:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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42 --maxDropFraction '$output_filter_options.maxDropFraction'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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43 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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44 #if $processing_options.byStrand:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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45 --byStrand '$processing_options.byStrand'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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46 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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47 #if $processing_options.noPolish:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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48 --noPolish '$processing_options.noPolish'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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49 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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50 #if $processing_options.richQVs:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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51 --richQVs '$processing_options.richQVs'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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52 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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53 #if $if_log.log_options == "yes":
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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54 --logFile '$log_output'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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55 --logLevel '$if_log.loglevel'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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56 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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57 #if $output_options.reportFile:
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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58 --reportFile ccs_report.txt
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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59 #end if
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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60 input.bam
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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61 output.bam
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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62 && mv output.bam '$bam_output'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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63 && mv ccs_report.txt '$report_output'
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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64 2>&1
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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65
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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66 ]]></command>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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67 <inputs>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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68 <param name="input_file" type="data" format="bam" label="Input Subreads" help="Subreads (subreads.bam)"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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69 <section name="input_filter_options" title="Input Filter Options" expanded="False">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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70 <param argument="--minLength" type="integer" value="10" label="Minimum length" help="Minimum draft length before polishing. [10]" />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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71 <param argument="--maxLength" type="integer" value="21000" label="Maximum length" help="Maximum draft length before polishing. [21000]"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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72 <param argument="--minPasses" type="integer" value="3" label="Minimum number of subreads" help="Minimum number of subreads required to generate CCS. [3]" />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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73 <param argument="--minIdentity" type="float" value="0.82" label="top N passes" help="Minimum identity of a subread aligned to the draft consensus to use it for polishing. 0 disables this filter. [0.82]" />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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74 <param argument="--minSnr" type="float" value="2.5" label="Minimum SNR of subreads" help="Minimum SNR of subreads to use for generating CCS [2.5]"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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75 <param argument="--zmws" type="text" value="all" label="Generate CCS for the provided comma-separated hole number ranges only." help="Default=all" />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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76 </section>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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77 <section name="model_override_options" title="Model Override Options" expanded="False">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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78 <param argument="--modelPath" type="data" format="txt" optional="True" label="Model File" help="a model file or directory containing model files." />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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79 <param argument="--modelSpec" type="text" value="" optional="True" label="Chemistry" help="Name of chemistry or model to use, overriding default selection."/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
galaxy-australia
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80 </section>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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81 <section name="processing_options" title="Processing Options" expanded="False">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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82 <param argument="--byStrand" type="boolean" truevalue="--byStrand" falsevalue="" checked="false" label="Generate a consensus for each strand." />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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83 <param argument="--noPolish" type="boolean" truevalue="--noPolish" falsevalue="" checked="false" label="Only output the initial template derived from the POA (faster, less accurate)." />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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84 <param argument="--richQVs" type="boolean" truevalue="--richQVs" falsevalue="" checked="false" label="Emit dq, iq, and sq rich quality tracks." />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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85 </section>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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86 <section name="output_filter_options" title="Output Flter Options" expanded="False">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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87 <param argument="--minPredictedAccuracy" type="float" value="0.9" label="Mininum predicted accurary" help="i.e 0.9"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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88 <param argument="--minReadScore" type="float" value="0.75" label="Minimum read score of input subreads" help="i.e 0.75"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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89 <param argument="--maxDropFraction" type="float" value="0.34" label="Maximum fraction of subreads dropped by polishing (not input filters) before skipping ZMW." help="i.e 0.34" />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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90 </section>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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91 <section name="output_options" title="Output Files Options" expanded="False">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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92 <param argument="--reportFile" type="boolean" truevalue="True" falsevalue="False" checked="False" label="write the results report."/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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93 </section>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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94 <conditional name="if_log">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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95 <param type="select" name="log_options" label="show log option">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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96 <option value="yes">Yes</option>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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97 <option value="no" selected="true">No</option>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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98 </param>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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99 <when value="yes">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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100 <param argument="--logLevel" name="loglevel" type="select" label="Log Level">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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101 <option selected="True" value="WARN">WARN</option>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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102 <option value="TRACE">TRACE</option>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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103 <option value="DEBUG">DEBUG</option>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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104 <option value="INFO">INFO</option>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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105 <option value="FATAL">FATAL</option>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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106 </param>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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107 </when>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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108 <when value="no">
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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109 </when>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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110 </conditional>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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111 </inputs>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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112 <outputs>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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113 <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: CCS reads in BAM format"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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114 <data format="txt" name="report_output" label="${tool.name} on ${on_string}: CCS reads report"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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115 <data format="txt" name="log_output" label="${tool.name} on ${on_string}: log" >
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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116 <filter>if_log['log_options'] == 'yes' </filter>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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117 </data>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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118 </outputs>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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119 <tests>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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120 <test><!-- test with default settings -->
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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121 <param name="input_file" ftype="bam" value="input.subreads.bam"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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122 <output name="bam_output" ftype="bam" file="output.bam" />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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123 <output name="log_output" ftype="txt" file="log.txt" />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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124 <output name="report_output" ftype="txt" file="report.txt" />
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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125 </test>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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126 </tests>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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127 <help><![CDATA[
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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128 @PBCCS_OVERVIEW@
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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129
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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130 For detailed information on psp-gen, click here_, or view the license_.
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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131
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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132 .. _here: https://github.com/nlhepler/pbccs
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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133 .. _license: https://github.com/nlhepler/pbccs/blob/master/LICENSE
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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134
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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135 **Command Documentation**
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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136
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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137 CCS will generate consensus sequence.
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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138
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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139
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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140 ]]></help>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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141 <expand macro="citations"/>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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142 </tool>
f159c3da2ffc "planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/pbccs commit 5ba0af2de1e1ce7b7a8ed3eb4042f5fec366c234"
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143