Mercurial > repos > cristian > notos
diff KDEanalysis.xml @ 0:1535ffddeff4 draft
planemo upload commit a7ac27de550a07fd6a3e3ea3fb0de65f3a10a0e6-dirty
author | cristian |
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date | Thu, 07 Sep 2017 08:51:57 -0400 |
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children | cb8bac9d0d37 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/KDEanalysis.xml Thu Sep 07 08:51:57 2017 -0400 @@ -0,0 +1,80 @@ +<tool id="notos" name="Analyse CpGo/e ratios" version="1.0.0"> + <requirements> + <requirement type="package" version="3.2.1">R</requirement> + <requirement type="package" version="1.0.0">notos</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + Rscript ${__tool_directory__}/KDEanalysis.r + -o $fracOutl + -d $minDist + -c $confLevel + -m $modeMass + -b $bandWidth + #if $bootstrap == "TRUE" + -B + #end if + -r $BSrep + #if $nofew == "TRUE" + -f + #end if + "$species" + $cpgoe + ]]></command> + <inputs> + <param name="species" size="30" type="text" value="my_species" label="Species name" /> + <param name="cpgoe" type="data" format="tabular" /> + <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" /> + <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" /> + <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" /> + <param name="modeMass" type="float" value="0.05" help="minimum probability mass of a mode " label= "minimum probability mass of a mode" /> + <param name="bandWidth" type="float" value="1.06" help="bandwidth constant for kernels " label= "bandwidth constant for kernels" /> + <param name="bootstrap" type="boolean" truevalue="TRUE" falsevalue="FALSE" help="calculate confidence intervals of mode positions using bootstrap" label= "bootstrap confidence intervals?" /> + <param name="BSrep" type="integer" value="1500" help="number of bootstrap repetitions " label= "number of bootstrap repetitions " /> + <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" /> + </inputs> + <outputs> + <data name="summary" format="tabular" from_work_dir="summary.csv" label="Summary on ${on_string}" /> + <data name="outlierHist" format="pdf" from_work_dir="outliers_hist.pdf" label="Outlier Histogram on ${on_string}"/> + <data name="cutoff" format="tabular" from_work_dir="outliers_cutoff.csv" label="Outlier cutoff on ${on_string}" /> + <data name="peaks" format="tabular" from_work_dir="modes_basic_stats.csv" label="Peaks on ${on_string}" /> + <data name="kde" format="pdf" from_work_dir="KDE.pdf" label="KDE analysis on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="cpgoe" value="10_std_unif.txt"/> + <output name="cutoff1" file="outliers_cutoff.csv"/> + <!-- + <output name="outlierHist" file="outliers_hist.pdf"/> + <output name="kde" file="KDE.pdf"/> + --> + </test> + </tests> + <help><![CDATA[ +Model the distribution of CpG o/e ratios using Kernel Density Estimation. + +Parameters:: + + "-o", "--frac-outl" maximum fraction of CpGo/e ratios excluded as outliers [default 0.01] + "-d", "--min-dist" minimum distance between modes, modes that are closer are joined [default 0.2] + "-c", "--conf-level" level of the confidence intervals of the mode positions [default 0.95] + "-m", "--mode-mass" minimum probability mass of a mode [default 0.05] + "-b", "--band-width" bandwidth constant for kernels [default 1.06] + "-B", "--bootstrap" calculate confidence intervals of mode positions using bootstrap. + "-r", "--bootstrap-reps" number of bootstrap repetitions [default 1500] + "-p", "--peak-file" name of the output file describing the peaks of the KDE [default peaks.csv] + "-s", "--bootstrap-file" Name of the output file with bootstrap values [default "bootstrap.csv"] + "-H", "--outlier-hist-file" Outliers histogram file [default outliers_hist.pdf] + "-C", "--cutoff-file" Outliers cutoff file [default outliers_cutoff.csv] + "-k", "--kde-file" Kernel density estimation graph [default KDE.pdf] + + + ]]></help> + <citations> + <citation> + <citation type="doi">10.1101/180463</citation> + </citation> + </citations> +</tool>