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1 <tool id="pathoscope_id" name="Pathoscope ID" version="0.1.0">
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2 <description>Pathoscope ID</description>
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3 <requirements>
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4 <requirement type="package" version="2.0.6">pathoscope</requirement>
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5 </requirements>
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6 <command> <![CDATA[ln -s '$alignFile' align.sam &&
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7 pathoscope ID -alignFile align.sam -fileType $fileType -piPrior $piPrior -thetaPrior $thetaPrior
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8 -scoreCutoff $scoreCutoff -emEpsilon $emEpsilon -maxIter $maxIter
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9 #unless $updatedAlignFile
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10 --noUpdatedAlignFile
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11 #end unless
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12 #unless $displayCutoff
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13 --noDisplayCutoff
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14 #end unless
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15 #if $outMatrix
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16 --outMatrix
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17 #end if]]>
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18 </command>
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19 <inputs>
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20 <param format="sam" name="alignFile" type="data" label="Align File"/>
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21 <param name="fileType" type="select" label="Choose file type">
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22 <option value="sam">Sam File</option>
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23 </param>
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24 <param name="thetaPrior" type="integer" value="0"
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25 optional="true"
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26 help="EM Algorithm Theta Prior equivalent to adding n non-unique reads" label="thetaPrior">
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27 </param>
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28 <param name="piPrior" type="integer" value="0"
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29 optional="true"
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30 help="EM Algorithm Pi Prior equivalent to adding n unique reads" label="piPrior">
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31 </param>
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32 <param name="updatedAlignFile" type="boolean" truevalue="yes" falsevalue="no" checked="on" label="Generate updated align file?"/>
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33 <param name="displayCutoff" type="boolean" truevalue="yes" falsevalue="no" checked="on" label="Cutoff display genomes?" help="cutoff display of genomes, even if it is insignificant"/>
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34 <param name="outMatrix" type="boolean" truevalue="yes" falsevalue="no" checked="off" label="Output alignment matrix"/>
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35 <param name="scoreCutoff" type="float" value="0.01" help="Score Cutoff"/>
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36 <param name="emEpsilon" type="float" value="1e-7" help="EM Algorithm Epsilon cutoff"/>
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37 <param name="maxIter" type="integer" value="50" help="EM Algorithm maximum iterations"/>
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38 </inputs>
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39 <outputs>
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40 <data format="tsv" name="tableFile" from_work_dir="pathoid-sam-report.tsv" />
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41 <data format="sam" name="realignFile" from_work_dir="updated_align.sam" />
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42 </outputs>
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43
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44 <tests>
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45 <test>
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46 <param name="alignFile" value="MAP_3852_align.sam"/>
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47 <param name="fileType" value="sam" />
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48 <param name="thetaPrior" value="0" />
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49 <param name="piPrior" value="0" />
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50 <param name="updatedAlignFile" checked="on" />
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51 <param name="displayCutoff" checked="on" />
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52 <param name="outMatrix" checked="off" />
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53 <param name="scoreCutoff" value="0.01" />
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54 <param name="emEpsilon" value="1e-7" />
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55 <param name="maxIter" value="50" />
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56 <output name="tsv" file="pathoid-sam-report.tsv"/>
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57 <output name="sam" file="updated_align.sam"/>
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58 </test>
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59 </tests>
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60
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61 <help>
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62 The PathoID module is the core of the PathoScope pipeline. The key is to identify
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63 reads with unique alignments and use them to guide the reassignment of reads with ambiguous
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64 alignments.
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65 </help>
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66 <citations>
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67 <citation type="doi">10.1101/gr.150151.112</citation>
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68 <citation type="doi">10.1186/2049-2618-2-33</citation>
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69 <citation type="doi">10.1186/1471-2105-15-262</citation>
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70 <citation type="doi">10.4137/CIN.S13890</citation>
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71 </citations>
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72
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73 </tool>
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