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1 <tool id="smrtpipe_filter" name="SMRTpipe Filter" version="1.0.0">
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2 <description>Produce filtered reads from a set of PacBio primary analysis outputs.</description>
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3 <command interpreter="python">
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4 smrtpipe_galaxy.py --output=data/filtered_subreads.fasta --galaxy_output=${outfile} ${iniFile}
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5 </command>
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6 <inputs>
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7 <conditional name="source">
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8 <param name="input_source" type="select" label="Choose the source for the analysis inputs">
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9 <option value="path">Path to fofn or multiple bas.h5 paths</option>
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10 <option value="history">History</option>
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11 </param>
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12 <when value="path">
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13 <repeat name="inputFiles" title="Input files">
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14 <param name="path" type="text" label="File path" size="75"/>
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15 </repeat>
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16 </when>
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17 <when value="history">
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18 <param name="input1" type="data" format="tabular" label="File containing input paths" />
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19 </when>
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20 </conditional>
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21 <param name="minimum_readlength" type="integer" value="50" label="Minimum raw readlength" />
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22 <param name="minimum_readscore" type="float" value="0.75" label="Minimum read quality" />
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23 </inputs>
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24 <configfiles>
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25 <configfile name="iniFile">
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26 [input]
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27 #if $source.input_source=="history":
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28 #for $l in open($source.input1.file_name,'r'):
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29 $l
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30 #end for
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31 #else
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32 #for $p in $source.inputFiles
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33 ${p.path}
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34 #end for
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35 #end if
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36
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37 [S_Filter]
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38 filters=MinRL=${minimum_readlength},MinReadScore=${minimum_readscore}
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39 </configfile>
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40 </configfiles>
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41 <outputs>
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42 <data name="outfile" format="fasta" label="Filtered subreads" />
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43 </outputs>
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44 <help>
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45
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46 **What it does**
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47
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48 Filters PacBio bas.h5 files and produces a FASTA file of filtered subreads.
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49
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50 In PacBio SMRT sequencing, the template format is a SMRTbell: a circular
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51 molecule with adapters at two locations in the circle. The subreads are the
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52 portions of the read between adapters.
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53
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54 **Parameter list**
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55
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56 Minimum readlength
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57 Only keep reads from ZMWs that produced this many bases or more.
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58
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59 Minimum read quality
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60 Only keep reads with overall quality scores of this value or more. The read quality score is a *de novo* prediction of the accuracy of the read.
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61
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62 **Output**
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63
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64 FASTA file of filtered reads.
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65
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66 </help>
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67 </tool>
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