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1 <tool id="smrtpipe_hybrid" name="AHA" version="1.0.0">
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2 <description>Assemble contigs from a set of contigs and PacBio reads.</description>
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3 <command interpreter="python">
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4 smrtpipe_galaxy.py --nproc=24 --dat_extension=fasta --output=data/scaffold.fasta --galaxy_output=${outfile} ${iniFile}
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5 </command>
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6 <!--
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7 <command>cp ${iniFile} ${outfile}</command>
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8 -->
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9 <inputs>
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10 <param name="contigs" format="fasta" type="data" label="Starting Contigs"/>
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11 <param name="reads" format="fasta" type="data" label="PacBio Reads"/>
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12 <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/>
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13 </inputs>
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14 <configfiles>
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15 <configfile name="iniFile">
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16 [input]
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17 assembled_contigs:${contigs}
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18 file:${reads}
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19
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20 [HybridAssembly]
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21 instrumentModel=RS
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22 cleanup=False
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23 untangler=pacbio
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24 #set $schedule2 = $schedule.replace('X',';')
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25 paramSchedule=${schedule2}
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26 dontFillin=False
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27 longReadsAsStrobe=True
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28 exactQueryIds=True
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29 rm4Opts=-minMatch 7 -minFrac 0.1 -minPctIdentity 65 -bestn 10 -noSplitSubreads
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30 numberProcesses=16
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31 cluster=False
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32 minRepeatLength=100000
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33 </configfile>
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34 </configfiles>
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35 <outputs>
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36 <data name="outfile" format="fasta" label="Hybrid assembly contigs from ${on_string}"/>
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37 </outputs>
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38 <help>
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39
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40 **What it does**
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41
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42 The AHA assembly algorithm is an AMOS_-based pipeline
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43 for finishing bacterial-sized
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44 genomes using draft contigs and PacBio reads.
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45
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46 .. _AMOS: http://sourceforge.net/apps/mediawiki/amos
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47
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48 **Parameter list**
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49
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50 Parameter schedule
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51 The parameter schedule is a semi-colon delimited list of triples. Each triple represents an iteration of hybrid assembly (alignment/scaffolding/gap-filling). The three paremeters for each iteration are the Z-score, number of reads required to define a link, and the minimum length of subreads used in links.
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52
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53 **Output**
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54
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55 FASTA file containing scaffolded and gap-filled contigs resulting from the
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56 hybrid assembly.
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57
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58 </help>
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59 </tool>
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