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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
author iuc
date Mon, 02 Oct 2023 13:23:59 +0000
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ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.1.1</token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">baredsc</requirement>
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7 <requirement type="package" version="1.12">gzip</requirement>
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8 </requirements>
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9 <version_command><![CDATA[baredSC_1d --version]]></version_command>
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10 </xml>
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11 <xml name="helpcitations">
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12 <help><![CDATA[
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14 .. class:: infomark
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16 **BARED (Bayesian Approach to Retreive Expression Distribution of) Single Cell**
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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.
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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ac9434b9fc27 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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22 This is a description of the figure with the results.
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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)``).
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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).
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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27
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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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29
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30 ]]></help>
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31 <citations>
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32 <citation type="doi">10.1186/s12859-021-04507-8</citation>
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33 </citations>
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34 </xml>
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35 <xml name="edam_topics">
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36 <edam_topics>
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37 <edam_topic>topic_3170</edam_topic>
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38 <edam_topic>topic_4028</edam_topic>
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39 <edam_topic>topic_2269</edam_topic>
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40 </edam_topics>
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41 </xml>
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42 <xml name="macro_input_counts">
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43 <conditional name="input_counts">
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44 <param name="filetype" type="select" label="Input type">
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45 <option value="tabular">Tabular</option>
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46 <option value="anndata">Anndata (for example from Scanpy)</option>
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47 </param>
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48 <when value="tabular">
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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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50 </when>
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51 <when value="anndata">
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52 <param argument="--inputAnnData" type="data" format="anndata" label="AnnData containing raw counts" />
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53 </when>
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54 </conditional>
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55 </xml>
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56 <xml name="macro_single_gene">
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57 <param argument="--geneColName" type="text" value="" label="Name of the column with gene counts."/>
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58 </xml>
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59 <xml name="macro_two_genes">
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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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61 <param argument="--geneYColName" type="text" value="" label="Name of the column with gene counts for gene in y."/>
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62 </xml>
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63 <xml name="macro_filter_cells">
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64 <conditional name="filter">
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65 <param name="nb" type="select" label="How many filters columns do you need?">
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66 <option value="0">0 (keep all cells from file)</option>
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67 <option value="1">1</option>
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68 <option value="2">2</option>
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69 <option value="3">3</option>
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70 </param>
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71 <when value="0"/>
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72 <when value="1">
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73 <param argument="--metadata1ColName" type="text" value="" label="Name of the column with first filter."/>
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74 <param argument="--metadata1Values" type="text" value="" label="Values accepted in this column (separated by comma)."/>
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75 </when>
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76 <when value="2">
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77 <param argument="--metadata1ColName" type="text" value="" label="Name of the column with first filter."/>
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78 <param argument="--metadata1Values" type="text" value="" label="Values accepted in this column (separated by comma)."/>
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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."/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
88 <param argument="--metadata3Values" type="text" value="" label="Values accepted in this column (separated by comma)."/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
89 </when>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
90 </conditional>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
91 </xml>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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92 <xml name="macro_MCMC_params_common_axis" token_axis="x">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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."/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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."/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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." />
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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."/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
97 </xml>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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98 <xml name="macro_scale_seed">
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99 <conditional name="scale">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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100 <param name="type" type="select" label="Scale for gene expression">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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101 <option value="Seurat">Like in Seurat (log(1+targetSum*X))</option>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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102 <option value="log">simply log</option>
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diff changeset
103 </param>
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diff changeset
104 <when value="Seurat">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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105 <param argument="--targetSum" type="float" value="10000" label="targetSum" help="use 0 for the median of nRNA_Counts"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
106 </when>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
107 <when value="log"/>
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diff changeset
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"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
110 </xml>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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111 <xml name="macro_MCMC_common_baredSC">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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112 <param argument="--nnorm" type="integer" min="1" value="2" label="Number of Gaussians to fit." />
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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113 <param argument="--nsampMCMC" type="integer" min="1" value="100000" label="Number of samplings (iterations) of MCMC." />
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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114 <conditional name="automaticRestart">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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115 <param name="set_minNeff" type="select" label="Auto-rerun in case of obvious non-convergence">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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116 <option value="yes">Yes (the job may never stop)</option>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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117 <option value="no">No</option>
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diff changeset
118 </param>
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diff changeset
119 <when value="yes">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
121 </when>
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diff changeset
122 <when value="no"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
123 </conditional>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
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"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
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">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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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diff changeset
133 </param>
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134 <param argument="--title" type="text" value="" label="Title to set to all figures."/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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136 <param argument="--nsampInPlot" type="integer" value="100000" min="1" label="Approximate number of samples to use in plots"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
137 </xml>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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138 <xml name="macro_prettybins_1d">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
140 </xml>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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141 <xml name="macro_prettybins_axis" token_axis="x">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
143 </xml>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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144 <xml name="macro_splity">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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.">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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146 <validator type="regex">(-?[0-9]+( -?[0-9]+)*)?</validator>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
151 </xml>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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152 <xml name="macro_advanced_common_axis" token_axis="x" token_default_osamppdf="5">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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." />
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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."/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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diff changeset
155 </xml>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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." />
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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158 <param argument="--nis" type="integer" value="1000" label="Size of sampling of random parameters in logevidence evaluation." />
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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159 </xml>
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160 <xml name="macro_advanced_common_baredSC">
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diff changeset
161 <conditional name="burn">
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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>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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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diff changeset
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)" />
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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169 <param argument="--T0BurnMCMC" type="float" value="100" label="Initial temperature in the burning phase of MCMC" min="1"/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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">
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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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."/>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
175 </xml>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
176 <token name="@REQUIRED_INPUTS_1D@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
177 #if str( $input_counts.filetype ) == "tabular":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
178 --input '$input_counts.input'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
179 #elif str( $input_counts.filetype ) == "anndata":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
180 --inputAnnData '$input_counts.inputAnnData'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
181 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
182 --geneColName '$geneColName'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
183 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
184 <token name="@REQUIRED_INPUTS_2D@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
185 #if str( $input_counts.filetype ) == "tabular":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
186 --input '$input_counts.input'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
187 #elif str( $input_counts.filetype ) == "anndata":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
188 --inputAnnData '$input_counts.inputAnnData'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
189 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
190 --geneXColName '$geneXColName'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
191 --geneYColName '$geneYColName'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
192 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
193 <token name="@FILTER_CELLS@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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diff changeset
194 #if str( $filter.nb ) == "1":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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195 --metadata1ColName '$filter.metadata1ColName'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
196 --metadata1Values '$filter.metadata1Values'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
197 #elif str( $filter.nb ) == "2":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
198 --metadata1ColName '$filter.metadata1ColName'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
199 --metadata1Values '$filter.metadata1Values'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
200 --metadata2ColName '$filter.metadata2ColName'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
201 --metadata2Values '$filter.metadata2Values'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
202 #elif str( $filter.nb ) == "3":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
203 --metadata1ColName '$filter.metadata1ColName'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
204 --metadata1Values '$filter.metadata1Values'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
205 --metadata2ColName '$filter.metadata2ColName'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
206 --metadata2Values '$filter.metadata2Values'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
207 --metadata3ColName '$filter.metadata3ColName'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
208 --metadata3Values '$filter.metadata3Values'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
209 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
210 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
211 <token name="@MCMC_1D@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
212 --xmin $MCMC.xmin
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
213 --xmax $MCMC.xmax
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
214 --xscale '$MCMC.scale.type'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
215 #if str( $MCMC.scale.type ) == "Seurat":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
216 --targetSum $MCMC.scale.targetSum
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
217 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
218 --nx $MCMC.nx
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
219 --minScale $MCMC.minScalex
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
220 --seed $MCMC.seed
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
221 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
222 <token name="@MCMC_2D@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
223 --xmin $MCMC.xmin
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
224 --xmax $MCMC.xmax
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
225 --nx $MCMC.nx
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
226 --minScalex $MCMC.minScalex
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
227 --ymin $MCMC.ymin
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
228 --ymax $MCMC.ymax
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
229 --ny $MCMC.ny
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
230 --minScaley $MCMC.minScaley
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
231 --scale '$MCMC.scale.type'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
232 #if str( $MCMC.scale.type ) == "Seurat":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
233 --targetSum $MCMC.scale.targetSum
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
234 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
235 --seed $MCMC.seed
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
236 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
237 <token name="@BAREDSC_COMMON@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
238 --nnorm $MCMC.nnorm
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
239 --nsampMCMC $MCMC.nsampMCMC
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
240 #if str( $MCMC.automaticRestart.set_minNeff ) == "yes":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
241 --minNeff $MCMC.automaticRestart.minNeff
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
242 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
243 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
244 <token name="@PLOTS@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
245 #if str( $plots.title ) != '':
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
246 --title '$plots.title'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
247 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
248 #if $plots.removeFirstSamples != -1:
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
249 --removeFirstSamples $plots.removeFirstSamples
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
250 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
251 --nsampInPlot $plots.nsampInPlot
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
252 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
253 <token name="@PRETTYBINS_1D@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
254 #if $plots.prettyBins != -1:
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
255 --prettyBins $plots.prettyBins
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
256 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
257 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
258 <token name="@PRETTYBINS_SPLITY_COLORSCALE_2D@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
259 #if $plots.prettyBinsx != -1:
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
260 --prettyBinsx $plots.prettyBinsx
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
261 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
262 #if $plots.prettyBinsy != -1:
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
263 --prettyBinsy $plots.prettyBinsy
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
264 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
265 ## splity is space separated floats
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
266 #if str($plots.splity) != '':
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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267 --splity $plots.splity
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268 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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269 #if str($plots.log1pColorScale) != '':
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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270 '$plots.log1pColorScale'
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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271 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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272 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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273 <token name="@ADVANCED_COMMON_X@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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274 --osampx $advanced.osampx
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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275 --osampxpdf $advanced.osampxpdf
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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276 --coviscale $advanced.coviscale
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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277 --nis $advanced.nis
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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278 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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279 <token name="@ADVANCED_COMMON_COMPLEMENT_2D@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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280 --osampy $advanced.osampy
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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281 --osampypdf $advanced.osampypdf
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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282 --scalePrior $advanced.scalePrior
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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283 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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284 <token name="@ADVANCED_BAREDSC_COMMON@" ><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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285 #if str( $advanced.burn.custom ) == "yes":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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286 #if str( $advanced.burn.nsampBurnMCMC ) != "-1":
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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287 --nsampBurnMCMC $advanced.burn.nsampBurnMCMC
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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288 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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289 --T0BurnMCMC $advanced.burn.T0BurnMCMC
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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290 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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291 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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292 <token name="@COMBINE_OUTPUTS@"><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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293 --outputs
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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294 #for $i, $output in enumerate($MCMC.outputs):
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295 $i
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296 #end for
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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297 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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298 <token name="@ORDER_OUTPUTS_1D@"><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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299 mv baredSC_pdf.txt output &&
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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300 mv baredSC.$plots.image_file_format baredSC &&
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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301 gunzip baredSC_means.txt.gz
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302 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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303 <token name="@ORDER_OUTPUTS_2D@"><![CDATA[
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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304 mv baredSC_pdf2d.txt output &&
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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305 mv baredSC_pdf2d_flat.txt output &&
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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306 mv baredSC.$plots.image_file_format baredSC
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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307 #if str($plots.splity) != '':
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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308 #for $value in str($plots.splity).split(' '):
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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309 && mv baredSC_split'$value'.txt baredSC_split'$value'_pdf.txt
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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310 #end for
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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311 #end if
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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312 ]]></token>
ac9434b9fc27 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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313 </macros>