Mercurial > repos > iuc > baredsc_2d
annotate macros.xml @ 0:aa379e925d98 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
| author | iuc |
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| date | Mon, 02 Oct 2023 13:23:27 +0000 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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1 <macros> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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2 <token name="@TOOL_VERSION@">1.1.1</token> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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3 <token name="@VERSION_SUFFIX@">0</token> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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4 <xml name="requirements"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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5 <requirements> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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6 <requirement type="package" version="@TOOL_VERSION@">baredsc</requirement> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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7 <requirement type="package" version="1.12">gzip</requirement> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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8 </requirements> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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9 <version_command><![CDATA[baredSC_1d --version]]></version_command> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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10 </xml> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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11 <xml name="helpcitations"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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12 <help><![CDATA[ |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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13 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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14 .. class:: infomark |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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15 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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16 **BARED (Bayesian Approach to Retreive Expression Distribution of) Single Cell** |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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17 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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18 baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. It uses the raw counts and the total number of UMI for each cell. The PDF is approximated by a number of 1d or 2d gaussians provided by the user. The likelihood is estimated using the asumption that the raw counts follow a Poisson distribution of parameter equal to the proportion of mRNA for the gene in the cell multiplied by the total number of UMI identified in this cell. |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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19 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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20 To get a description of outputs, please read the `Documentation <https://baredsc.readthedocs.io/en/latest/index.html>`_ |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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21 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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22 This is a description of the figure with the results. |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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23 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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24 - When the 1d version is used, it displays the mean PDF in solid red line, the median in black dashed lines (/!\backslash the integral of the median is not equal to 1) with the confidence interval of 1 sigma (68%), 2 sigma (95%) and 3 sigma (99.7%) as well as in green, the kernel density estimate of the input values, the detected expression (``log(1 + targetSum * raw / total UMI)``). |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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25 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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26 - When the 2d version is used, it displays the PDF as a heatmap as well as a projection on the x and y axis. On the projection, the confidence interval 68% is indicated as a shaded area as well as the mean with a solid red line and the median with a dashed black line. On the top right corner, the correlation is indicated with the confidence interval 68% as well as a confidence interval on the one-sided p-value (the probability that the correlation is the opposite sign of the mean, one sigma confidence interval). |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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27 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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28 Usually you should run baredSC_1d or baredSC_2d with 1 to 4 gaussians. Then you combine the different models with combineMultipleModels_1d or combineMultipleModels_2d. |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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29 |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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30 ]]></help> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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31 <citations> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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32 <citation type="doi">10.1186/s12859-021-04507-8</citation> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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33 </citations> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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34 </xml> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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35 <xml name="edam_topics"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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36 <edam_topics> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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37 <edam_topic>topic_3170</edam_topic> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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38 <edam_topic>topic_4028</edam_topic> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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39 <edam_topic>topic_2269</edam_topic> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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40 </edam_topics> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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41 </xml> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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42 <xml name="macro_input_counts"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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43 <conditional name="input_counts"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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44 <param name="filetype" type="select" label="Input type"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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45 <option value="tabular">Tabular</option> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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46 <option value="anndata">Anndata (for example from Scanpy)</option> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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47 </param> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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48 <when value="tabular"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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49 <param argument="--input" type="data" format="tabular" label="Input table (with header)" help="Expected format is one line per cell, columns with raw counts and one column 'nCount_RNA' with the total number of UMI per cell (optionally other meta data to filter)" /> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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50 </when> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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51 <when value="anndata"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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52 <param argument="--inputAnnData" type="data" format="anndata" label="AnnData containing raw counts" /> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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53 </when> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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54 </conditional> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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55 </xml> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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56 <xml name="macro_single_gene"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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57 <param argument="--geneColName" type="text" value="" label="Name of the column with gene counts."/> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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58 </xml> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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59 <xml name="macro_two_genes"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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60 <param argument="--geneXColName" type="text" value="" label="Name of the column with gene counts for gene in x."/> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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61 <param argument="--geneYColName" type="text" value="" label="Name of the column with gene counts for gene in y."/> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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62 </xml> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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63 <xml name="macro_filter_cells"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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64 <conditional name="filter"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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65 <param name="nb" type="select" label="How many filters columns do you need?"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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66 <option value="0">0 (keep all cells from file)</option> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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67 <option value="1">1</option> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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68 <option value="2">2</option> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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69 <option value="3">3</option> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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70 </param> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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71 <when value="0"/> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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72 <when value="1"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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73 <param argument="--metadata1ColName" type="text" value="" label="Name of the column with first filter."/> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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74 <param argument="--metadata1Values" type="text" value="" label="Values accepted in this column (separated by comma)."/> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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75 </when> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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76 <when value="2"> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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77 <param argument="--metadata1ColName" type="text" value="" label="Name of the column with first filter."/> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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78 <param argument="--metadata1Values" type="text" value="" label="Values accepted in this column (separated by comma)."/> |
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aa379e925d98
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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79 <param argument="--metadata2ColName" type="text" value="" label="Name of the column with second filter."/> |
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80 <param argument="--metadata2Values" type="text" value="" label="Values accepted in this column (separated by comma)."/> |
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81 </when> |
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82 <when value="3"> |
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83 <param argument="--metadata1ColName" type="text" value="" label="Name of the column with first filter."/> |
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84 <param argument="--metadata1Values" type="text" value="" label="Values accepted in this column (separated by comma)."/> |
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85 <param argument="--metadata2ColName" type="text" value="" label="Name of the column with second filter."/> |
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86 <param argument="--metadata2Values" type="text" value="" label="Values accepted in this column (separated by comma)."/> |
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87 <param argument="--metadata3ColName" type="text" value="" label="Name of the column with third filter."/> |
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88 <param argument="--metadata3Values" type="text" value="" label="Values accepted in this column (separated by comma)."/> |
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89 </when> |
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90 </conditional> |
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91 </xml> |
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92 <xml name="macro_MCMC_params_common_axis" token_axis="x"> |
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93 <param argument="--@AXIS@min" type="float" value="0" label="Minimum value to consider in @AXIS@ axis." help="Choose value small enough to go below smallest value."/> |
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94 <param argument="--@AXIS@max" type="float" value="2.5" label="Maximum value to consider in @AXIS@ axis." help="Choose value large enough to go above largest value."/> |
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95 <param argument="--n@AXIS@" type="integer" min="1" value="100" label="Number of values in @AXIS@ to check how your evaluated PDF is compatible with the model." help="Larger values will increase computing time while smaller values will decrease the resolution of your PDF." /> |
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96 <param argument="--minScale@AXIS@" type="float" value="0.1" label="Minimal value of the scale of Gaussians on @AXIS@" help="Cannot be smaller than max of twice the bin size of PDF evaluation and half the bin size on @AXIS@ axis."/> |
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97 </xml> |
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98 <xml name="macro_scale_seed"> |
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99 <conditional name="scale"> |
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100 <param name="type" type="select" label="Scale for gene expression"> |
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101 <option value="Seurat">Like in Seurat (log(1+targetSum*X))</option> |
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102 <option value="log">simply log</option> |
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103 </param> |
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104 <when value="Seurat"> |
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105 <param argument="--targetSum" type="float" value="10000" label="targetSum" help="use 0 for the median of nRNA_Counts"/> |
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106 </when> |
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107 <when value="log"/> |
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108 </conditional> |
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109 <param argument="--seed" type="integer" value="1" label="Seed value to control randomness." help="Change seed value to get new result"/> |
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110 </xml> |
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111 <xml name="macro_MCMC_common_baredSC"> |
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112 <param argument="--nnorm" type="integer" min="1" value="2" label="Number of Gaussians to fit." /> |
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113 <param argument="--nsampMCMC" type="integer" min="1" value="100000" label="Number of samplings (iterations) of MCMC." /> |
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114 <conditional name="automaticRestart"> |
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115 <param name="set_minNeff" type="select" label="Auto-rerun in case of obvious non-convergence"> |
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116 <option value="yes">Yes (the job may never stop)</option> |
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117 <option value="no">No</option> |
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118 </param> |
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119 <when value="yes"> |
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120 <param argument="--minNeff" type="float" value="200" label="Minimum number of effective samples to output result." help="If the number of effective samples is below this threshold, the MCMC is automatically rerun with 10 times more samples"/> |
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121 </when> |
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122 <when value="no"/> |
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123 </conditional> |
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124 </xml> |
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125 <xml name="combine_outputs" token_d="1"> |
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126 <param argument="--outputs" type="data" format="npz" label="Numpy archives from baredSC_@D@d with different number of Gaussians." multiple="true"/> |
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127 </xml> |
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128 <xml name="macro_plots"> |
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129 <param name="image_file_format" type="select" label="Image output format"> |
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130 <option value="png">png</option> |
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131 <option value="svg">svg</option> |
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132 <option value="pdf">pdf</option> |
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133 </param> |
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134 <param argument="--title" type="text" value="" label="Title to set to all figures."/> |
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135 <param argument="--removeFirstSamples" type="integer" value="-1" label="Number of samples to ignore before making the plots" help="Use -1 to use a fourth of the number of samples"/> |
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136 <param argument="--nsampInPlot" type="integer" value="100000" min="1" label="Approximate number of samples to use in plots"/> |
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137 </xml> |
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138 <xml name="macro_prettybins_1d"> |
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139 <param argument="--prettyBins" type="integer" value="-1" min="-1" label="Number of bins to use in plots." help="Use -1 to use the number of bins used in MCMC"/> |
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140 </xml> |
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141 <xml name="macro_prettybins_axis" token_axis="x"> |
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142 <param argument="--prettyBins@AXIS@" type="integer" value="-1" min="-1" label="Number of bins to use in @AXIS@ in plots." help="Use -1 to use the number of bins used in MCMC"/> |
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143 </xml> |
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144 <xml name="macro_splity"> |
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145 <param argument="--splity" type="text" value="" label="Threshold values separated by space to plot the density for genex for 2 categories in geney values" help="Leave empty if you don't need this type of analysis."> |
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146 <validator type="regex">(-?[0-9]+( -?[0-9]+)*)?</validator> |
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147 </param> |
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148 </xml> |
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149 <xml name="macro_colorscale"> |
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150 <param argument="--log1pColorScale" type="boolean" truevalue="--log1pColorScale" falsevalue="" checked="false" label="Enable to see regions in plot with low proportion of cells"/> |
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151 </xml> |
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152 <xml name="macro_advanced_common_axis" token_axis="x" token_default_osamppdf="5"> |
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153 <param argument="--osamp@AXIS@" type="integer" min="1" value="10" label="Oversampling factor of @AXIS@ values when evaluating PDF of Poisson distribution." /> |
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154 <param argument="--osamp@AXIS@pdf" type="integer" value="@DEFAULT_OSAMPPDF@" label="Oversampling factor of @AXIS@ values when evaluating PDF at each step of the MCMC."/> |
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155 </xml> |
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156 <xml name="macro_advanced_evidence"> |
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157 <param argument="--coviscale" type="float" value="1" label="Scale factor to apply to covariance of parameters to get random parameters in logevidence evaluation." /> |
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158 <param argument="--nis" type="integer" value="1000" label="Size of sampling of random parameters in logevidence evaluation." /> |
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159 </xml> |
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160 <xml name="macro_advanced_common_baredSC"> |
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161 <conditional name="burn"> |
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aa379e925d98
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162 <param name="custom" type="select" label="Custom parameters of the burning phase of MCMC"> |
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163 <option value="no">No</option> |
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164 <option value="yes">Yes</option> |
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165 </param> |
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166 <when value="no"/> |
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167 <when value="yes"> |
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168 <param argument="--nsampBurnMCMC" type="integer" value="-1" label="Number of samplings (iterations) in the burning phase of mcmc (Set -1 for a fourth of total number of samples)" /> |
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169 <param argument="--T0BurnMCMC" type="float" value="100" label="Initial temperature in the burning phase of MCMC" min="1"/> |
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170 </when> |
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171 </conditional> |
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172 </xml> |
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173 <xml name="macro_scaleprior"> |
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174 <param argument="--scalePrior" type="float" value="0.3" label="Scale of the truncnorm used in the prior for the correlation."/> |
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175 </xml> |
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176 <token name="@REQUIRED_INPUTS_1D@" ><![CDATA[ |
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177 #if str( $input_counts.filetype ) == "tabular": |
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178 --input '$input_counts.input' |
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179 #elif str( $input_counts.filetype ) == "anndata": |
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180 --inputAnnData '$input_counts.inputAnnData' |
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181 #end if |
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182 --geneColName '$geneColName' |
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183 ]]></token> |
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184 <token name="@REQUIRED_INPUTS_2D@" ><![CDATA[ |
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185 #if str( $input_counts.filetype ) == "tabular": |
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186 --input '$input_counts.input' |
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187 #elif str( $input_counts.filetype ) == "anndata": |
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188 --inputAnnData '$input_counts.inputAnnData' |
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189 #end if |
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190 --geneXColName '$geneXColName' |
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191 --geneYColName '$geneYColName' |
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192 ]]></token> |
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193 <token name="@FILTER_CELLS@" ><![CDATA[ |
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194 #if str( $filter.nb ) == "1": |
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195 --metadata1ColName '$filter.metadata1ColName' |
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196 --metadata1Values '$filter.metadata1Values' |
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197 #elif str( $filter.nb ) == "2": |
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198 --metadata1ColName '$filter.metadata1ColName' |
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199 --metadata1Values '$filter.metadata1Values' |
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200 --metadata2ColName '$filter.metadata2ColName' |
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201 --metadata2Values '$filter.metadata2Values' |
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202 #elif str( $filter.nb ) == "3": |
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203 --metadata1ColName '$filter.metadata1ColName' |
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204 --metadata1Values '$filter.metadata1Values' |
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205 --metadata2ColName '$filter.metadata2ColName' |
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206 --metadata2Values '$filter.metadata2Values' |
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207 --metadata3ColName '$filter.metadata3ColName' |
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208 --metadata3Values '$filter.metadata3Values' |
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209 #end if |
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210 ]]></token> |
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211 <token name="@MCMC_1D@" ><![CDATA[ |
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212 --xmin $MCMC.xmin |
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213 --xmax $MCMC.xmax |
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214 --xscale '$MCMC.scale.type' |
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215 #if str( $MCMC.scale.type ) == "Seurat": |
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216 --targetSum $MCMC.scale.targetSum |
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217 #end if |
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218 --nx $MCMC.nx |
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219 --minScale $MCMC.minScalex |
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220 --seed $MCMC.seed |
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221 ]]></token> |
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222 <token name="@MCMC_2D@" ><![CDATA[ |
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223 --xmin $MCMC.xmin |
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224 --xmax $MCMC.xmax |
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225 --nx $MCMC.nx |
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226 --minScalex $MCMC.minScalex |
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227 --ymin $MCMC.ymin |
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228 --ymax $MCMC.ymax |
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229 --ny $MCMC.ny |
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230 --minScaley $MCMC.minScaley |
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231 --scale '$MCMC.scale.type' |
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232 #if str( $MCMC.scale.type ) == "Seurat": |
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233 --targetSum $MCMC.scale.targetSum |
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234 #end if |
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235 --seed $MCMC.seed |
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236 ]]></token> |
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237 <token name="@BAREDSC_COMMON@" ><![CDATA[ |
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238 --nnorm $MCMC.nnorm |
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239 --nsampMCMC $MCMC.nsampMCMC |
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240 #if str( $MCMC.automaticRestart.set_minNeff ) == "yes": |
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241 --minNeff $MCMC.automaticRestart.minNeff |
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242 #end if |
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243 ]]></token> |
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244 <token name="@PLOTS@" ><![CDATA[ |
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245 #if str( $plots.title ) != '': |
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246 --title '$plots.title' |
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247 #end if |
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248 #if $plots.removeFirstSamples != -1: |
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249 --removeFirstSamples $plots.removeFirstSamples |
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250 #end if |
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251 --nsampInPlot $plots.nsampInPlot |
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252 ]]></token> |
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aa379e925d98
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253 <token name="@PRETTYBINS_1D@" ><![CDATA[ |
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254 #if $plots.prettyBins != -1: |
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255 --prettyBins $plots.prettyBins |
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256 #end if |
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257 ]]></token> |
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258 <token name="@PRETTYBINS_SPLITY_COLORSCALE_2D@" ><![CDATA[ |
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259 #if $plots.prettyBinsx != -1: |
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260 --prettyBinsx $plots.prettyBinsx |
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261 #end if |
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262 #if $plots.prettyBinsy != -1: |
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263 --prettyBinsy $plots.prettyBinsy |
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264 #end if |
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265 ## splity is space separated floats |
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266 #if str($plots.splity) != '': |
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267 --splity $plots.splity |
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268 #end if |
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269 #if str($plots.log1pColorScale) != '': |
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270 '$plots.log1pColorScale' |
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271 #end if |
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272 ]]></token> |
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273 <token name="@ADVANCED_COMMON_X@" ><![CDATA[ |
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274 --osampx $advanced.osampx |
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275 --osampxpdf $advanced.osampxpdf |
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276 --coviscale $advanced.coviscale |
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277 --nis $advanced.nis |
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278 ]]></token> |
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279 <token name="@ADVANCED_COMMON_COMPLEMENT_2D@" ><![CDATA[ |
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280 --osampy $advanced.osampy |
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281 --osampypdf $advanced.osampypdf |
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282 --scalePrior $advanced.scalePrior |
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283 ]]></token> |
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284 <token name="@ADVANCED_BAREDSC_COMMON@" ><![CDATA[ |
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285 #if str( $advanced.burn.custom ) == "yes": |
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286 #if str( $advanced.burn.nsampBurnMCMC ) != "-1": |
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287 --nsampBurnMCMC $advanced.burn.nsampBurnMCMC |
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288 #end if |
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289 --T0BurnMCMC $advanced.burn.T0BurnMCMC |
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290 #end if |
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291 ]]></token> |
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292 <token name="@COMBINE_OUTPUTS@"><![CDATA[ |
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293 --outputs |
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294 #for $i, $output in enumerate($MCMC.outputs): |
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295 $i |
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296 #end for |
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297 ]]></token> |
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298 <token name="@ORDER_OUTPUTS_1D@"><![CDATA[ |
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299 mv baredSC_pdf.txt output && |
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300 mv baredSC.$plots.image_file_format baredSC && |
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301 gunzip baredSC_means.txt.gz |
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302 ]]></token> |
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303 <token name="@ORDER_OUTPUTS_2D@"><![CDATA[ |
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304 mv baredSC_pdf2d.txt output && |
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305 mv baredSC_pdf2d_flat.txt output && |
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306 mv baredSC.$plots.image_file_format baredSC |
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307 #if str($plots.splity) != '': |
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308 #for $value in str($plots.splity).split(' '): |
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309 && mv baredSC_split'$value'.txt baredSC_split'$value'_pdf.txt |
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310 #end for |
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311 #end if |
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312 ]]></token> |
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313 </macros> |