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annotate KDEanalysis.xml @ 1:cb8bac9d0d37 draft default tip
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author | cristian |
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date | Thu, 07 Sep 2017 10:21:45 -0400 |
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1 <tool id="notos" name="Analyse CpGo/e ratios" version="1.0.0"> |
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2 <requirements> |
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3 <requirement type="package" version="3.2.1">R</requirement> |
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4 <requirement type="package" version="1.0.0">notos</requirement> |
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5 </requirements> |
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6 <stdio> |
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7 <exit_code range="1:" /> |
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8 </stdio> |
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9 <command><![CDATA[ |
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10 Rscript ${__tool_directory__}/KDEanalysis.r |
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11 -o $fracOutl |
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12 -d $minDist |
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13 -c $confLevel |
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14 -m $modeMass |
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15 -b $bandWidth |
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16 #if $bootstrap == "TRUE" |
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17 -B |
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18 #end if |
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19 -r $BSrep |
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20 #if $nofew == "TRUE" |
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21 -f |
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22 #end if |
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23 "$species" |
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24 $cpgoe |
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25 ]]></command> |
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26 <inputs> |
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27 <param name="species" size="30" type="text" value="my_species" label="Species name" /> |
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28 <param name="cpgoe" type="data" format="tabular" /> |
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29 <param name="fracOutl" type="float" value="0.01" help="maximum fraction of CpGo/e ratios excluded as outliers" label= "max fraction of CpGo/e ratios excluded as outliers" /> |
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30 <param name="minDist" type="float" value="0.2" help="minimum distance between modes. Modes that are closer are joined" label= "min distance between modes to join" /> |
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31 <param name="confLevel" type="float" value="0.95" help="level of the confidence intervals of the mode positions" label= "level of the confidence intervals of the mode positions" /> |
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32 <param name="modeMass" type="float" value="0.05" help="minimum probability mass of a mode " label= "minimum probability mass of a mode" /> |
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33 <param name="bandWidth" type="float" value="1.06" help="bandwidth constant for kernels " label= "bandwidth constant for kernels" /> |
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34 <param name="bootstrap" type="boolean" truevalue="TRUE" falsevalue="FALSE" help="calculate confidence intervals of mode positions using bootstrap" label= "bootstrap confidence intervals?" /> |
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35 <param name="BSrep" type="integer" value="1500" help="number of bootstrap repetitions " label= "number of bootstrap repetitions " /> |
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36 <param name="nofew" type="boolean" truevalue="TRUE" falsevalue="FALSE" help="Do not print warning message when few datapoint are given." label= "Supress few datapoint warning" /> |
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37 </inputs> |
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38 <outputs> |
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39 <data name="summary" format="tabular" from_work_dir="summary.csv" label="Summary on ${on_string}" /> |
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40 <data name="outlierHist" format="pdf" from_work_dir="outliers_hist.pdf" label="Outlier Histogram on ${on_string}"/> |
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41 <data name="cutoff" format="tabular" from_work_dir="outliers_cutoff.csv" label="Outlier cutoff on ${on_string}" /> |
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42 <data name="peaks" format="tabular" from_work_dir="modes_basic_stats.csv" label="Peaks on ${on_string}" /> |
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43 <data name="kde" format="pdf" from_work_dir="KDE.pdf" label="KDE analysis on ${on_string}" /> |
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44 </outputs> |
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45 <tests> |
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46 <test> |
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47 <param name="cpgoe" value="10_std_unif.txt"/> |
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48 <output name="cutoff1" file="outliers_cutoff.csv"/> |
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49 <!-- |
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50 <output name="outlierHist" file="outliers_hist.pdf"/> |
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51 <output name="kde" file="KDE.pdf"/> |
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52 --> |
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53 </test> |
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54 </tests> |
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55 <help><![CDATA[ |
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56 Model the distribution of CpG o/e ratios using Kernel Density Estimation. |
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57 |
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58 Parameters:: |
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59 |
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60 "-o", "--frac-outl" maximum fraction of CpGo/e ratios excluded as outliers [default 0.01] |
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61 "-d", "--min-dist" minimum distance between modes, modes that are closer are joined [default 0.2] |
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62 "-c", "--conf-level" level of the confidence intervals of the mode positions [default 0.95] |
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63 "-m", "--mode-mass" minimum probability mass of a mode [default 0.05] |
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64 "-b", "--band-width" bandwidth constant for kernels [default 1.06] |
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65 "-B", "--bootstrap" calculate confidence intervals of mode positions using bootstrap. |
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66 "-r", "--bootstrap-reps" number of bootstrap repetitions [default 1500] |
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67 "-p", "--peak-file" name of the output file describing the peaks of the KDE [default peaks.csv] |
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68 "-s", "--bootstrap-file" Name of the output file with bootstrap values [default "bootstrap.csv"] |
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69 "-H", "--outlier-hist-file" Outliers histogram file [default outliers_hist.pdf] |
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70 "-C", "--cutoff-file" Outliers cutoff file [default outliers_cutoff.csv] |
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71 "-k", "--kde-file" Kernel density estimation graph [default KDE.pdf] |
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72 |
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73 |
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74 ]]></help> |
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75 <citations> |
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76 <citation type="doi">10.1101/180463</citation> |
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77 </citations> |
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78 </tool> |