Mercurial > repos > jasper > pathoscope_id
comparison PathoID.xml @ 0:15f6593183bb draft default tip
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| author | jasper |
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| date | Thu, 13 Apr 2017 16:08:52 -0400 |
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| -1:000000000000 | 0:15f6593183bb |
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| 1 <tool id="pathoscope_id" name="Pathoscope ID" version="0.1.0"> | |
| 2 <description>Pathoscope ID</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.0.6">pathoscope</requirement> | |
| 5 </requirements> | |
| 6 <command> <![CDATA[ln -s '$alignFile' align.sam && | |
| 7 pathoscope ID -alignFile align.sam -fileType $fileType -piPrior $piPrior -thetaPrior $thetaPrior | |
| 8 -scoreCutoff $scoreCutoff -emEpsilon $emEpsilon -maxIter $maxIter | |
| 9 #unless $updatedAlignFile | |
| 10 --noUpdatedAlignFile | |
| 11 #end unless | |
| 12 #unless $displayCutoff | |
| 13 --noDisplayCutoff | |
| 14 #end unless | |
| 15 #if $outMatrix | |
| 16 --outMatrix | |
| 17 #end if]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param format="sam" name="alignFile" type="data" label="Align File"/> | |
| 21 <param name="fileType" type="select" label="Choose file type"> | |
| 22 <option value="sam">Sam File</option> | |
| 23 </param> | |
| 24 <param name="thetaPrior" type="integer" value="0" | |
| 25 optional="true" | |
| 26 help="EM Algorithm Theta Prior equivalent to adding n non-unique reads" label="thetaPrior"> | |
| 27 </param> | |
| 28 <param name="piPrior" type="integer" value="0" | |
| 29 optional="true" | |
| 30 help="EM Algorithm Pi Prior equivalent to adding n unique reads" label="piPrior"> | |
| 31 </param> | |
| 32 <param name="updatedAlignFile" type="boolean" truevalue="yes" falsevalue="no" checked="on" label="Generate updated align file?"/> | |
| 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"/> | |
| 34 <param name="outMatrix" type="boolean" truevalue="yes" falsevalue="no" checked="off" label="Output alignment matrix"/> | |
| 35 <param name="scoreCutoff" type="float" value="0.01" help="Score Cutoff"/> | |
| 36 <param name="emEpsilon" type="float" value="1e-7" help="EM Algorithm Epsilon cutoff"/> | |
| 37 <param name="maxIter" type="integer" value="50" help="EM Algorithm maximum iterations"/> | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data format="tsv" name="tableFile" from_work_dir="pathoid-sam-report.tsv" /> | |
| 41 <data format="sam" name="realignFile" from_work_dir="updated_align.sam" /> | |
| 42 </outputs> | |
| 43 | |
| 44 <tests> | |
| 45 <test> | |
| 46 <param name="alignFile" value="MAP_3852_align.sam"/> | |
| 47 <param name="fileType" value="sam" /> | |
| 48 <param name="thetaPrior" value="0" /> | |
| 49 <param name="piPrior" value="0" /> | |
| 50 <param name="updatedAlignFile" checked="on" /> | |
| 51 <param name="displayCutoff" checked="on" /> | |
| 52 <param name="outMatrix" checked="off" /> | |
| 53 <param name="scoreCutoff" value="0.01" /> | |
| 54 <param name="emEpsilon" value="1e-7" /> | |
| 55 <param name="maxIter" value="50" /> | |
| 56 <output name="tsv" file="pathoid-sam-report.tsv"/> | |
| 57 <output name="sam" file="updated_align.sam"/> | |
| 58 </test> | |
| 59 </tests> | |
| 60 | |
| 61 <help> | |
| 62 The PathoID module is the core of the PathoScope pipeline. The key is to identify | |
| 63 reads with unique alignments and use them to guide the reassignment of reads with ambiguous | |
| 64 alignments. | |
| 65 </help> | |
| 66 <citations> | |
| 67 <citation type="doi">10.1101/gr.150151.112</citation> | |
| 68 <citation type="doi">10.1186/2049-2618-2-33</citation> | |
| 69 <citation type="doi">10.1186/1471-2105-15-262</citation> | |
| 70 <citation type="doi">10.4137/CIN.S13890</citation> | |
| 71 </citations> | |
| 72 | |
| 73 </tool> |