Mercurial > repos > iuc > baredsc_combine_1d

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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 13:22:34 +0000
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7138ba54a2b6 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>
7138ba54a2b6 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.
7138ba54a2b6 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)``).
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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25
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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).
7138ba54a2b6 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>
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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">
7138ba54a2b6 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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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."/>
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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."/>
7138ba54a2b6 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." />
7138ba54a2b6 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."/>
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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"/>
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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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diff changeset
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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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>
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
172 </xml>
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
173 <xml name="macro_scaleprior">
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
174 <param argument="--scalePrior" type="float" value="0.3" label="Scale of the truncnorm used in the prior for the correlation."/>
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
175 </xml>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
177 #if str( $input_counts.filetype ) == "tabular":
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
178 --input '$input_counts.input'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
179 #elif str( $input_counts.filetype ) == "anndata":
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
180 --inputAnnData '$input_counts.inputAnnData'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
181 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
182 --geneColName '$geneColName'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
183 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
185 #if str( $input_counts.filetype ) == "tabular":
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
186 --input '$input_counts.input'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
187 #elif str( $input_counts.filetype ) == "anndata":
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
188 --inputAnnData '$input_counts.inputAnnData'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
189 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
190 --geneXColName '$geneXColName'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
191 --geneYColName '$geneYColName'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
192 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
194 #if str( $filter.nb ) == "1":
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
195 --metadata1ColName '$filter.metadata1ColName'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
196 --metadata1Values '$filter.metadata1Values'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
197 #elif str( $filter.nb ) == "2":
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
198 --metadata1ColName '$filter.metadata1ColName'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
199 --metadata1Values '$filter.metadata1Values'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
200 --metadata2ColName '$filter.metadata2ColName'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
201 --metadata2Values '$filter.metadata2Values'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
202 #elif str( $filter.nb ) == "3":
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
203 --metadata1ColName '$filter.metadata1ColName'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
204 --metadata1Values '$filter.metadata1Values'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
205 --metadata2ColName '$filter.metadata2ColName'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
206 --metadata2Values '$filter.metadata2Values'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
207 --metadata3ColName '$filter.metadata3ColName'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
208 --metadata3Values '$filter.metadata3Values'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
209 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
210 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
212 --xmin $MCMC.xmin
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
213 --xmax $MCMC.xmax
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
214 --xscale '$MCMC.scale.type'
7138ba54a2b6 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":
7138ba54a2b6 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
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
217 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
218 --nx $MCMC.nx
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
219 --minScale $MCMC.minScalex
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
220 --seed $MCMC.seed
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
221 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
223 --xmin $MCMC.xmin
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
224 --xmax $MCMC.xmax
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
225 --nx $MCMC.nx
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
226 --minScalex $MCMC.minScalex
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
227 --ymin $MCMC.ymin
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
228 --ymax $MCMC.ymax
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
229 --ny $MCMC.ny
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
230 --minScaley $MCMC.minScaley
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
231 --scale '$MCMC.scale.type'
7138ba54a2b6 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":
7138ba54a2b6 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
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
234 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
235 --seed $MCMC.seed
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
236 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
238 --nnorm $MCMC.nnorm
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
239 --nsampMCMC $MCMC.nsampMCMC
7138ba54a2b6 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":
7138ba54a2b6 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
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
242 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
243 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
245 #if str( $plots.title ) != '':
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
246 --title '$plots.title'
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
247 #end if
7138ba54a2b6 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:
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
249 --removeFirstSamples $plots.removeFirstSamples
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
250 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
251 --nsampInPlot $plots.nsampInPlot
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
252 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 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:
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
255 --prettyBins $plots.prettyBins
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
256 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
257 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 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:
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
260 --prettyBinsx $plots.prettyBinsx
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
261 #end if
7138ba54a2b6 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:
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
263 --prettyBinsy $plots.prettyBinsy
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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264 #end if
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265 ## splity is space separated floats
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266 #if str($plots.splity) != '':
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267 --splity $plots.splity
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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268 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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269 #if str($plots.log1pColorScale) != '':
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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270 '$plots.log1pColorScale'
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271 #end if
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272 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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274 --osampx $advanced.osampx
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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275 --osampxpdf $advanced.osampxpdf
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276 --coviscale $advanced.coviscale
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277 --nis $advanced.nis
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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278 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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280 --osampy $advanced.osampy
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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281 --osampypdf $advanced.osampypdf
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282 --scalePrior $advanced.scalePrior
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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283 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 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":
7138ba54a2b6 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":
7138ba54a2b6 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
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288 #end if
7138ba54a2b6 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
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290 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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291 ]]></token>
7138ba54a2b6 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[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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293 --outputs
7138ba54a2b6 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):
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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295 $i
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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296 #end for
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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297 ]]></token>
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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298 <token name="@ORDER_OUTPUTS_1D@"><![CDATA[
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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299 mv baredSC_pdf.txt output &&
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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300 mv baredSC.$plots.image_file_format baredSC &&
7138ba54a2b6 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>
7138ba54a2b6 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[
7138ba54a2b6 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 &&
7138ba54a2b6 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 &&
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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306 mv baredSC.$plots.image_file_format baredSC
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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307 #if str($plots.splity) != '':
7138ba54a2b6 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(' '):
7138ba54a2b6 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
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310 #end for
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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311 #end if
7138ba54a2b6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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312 ]]></token>
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313 </macros>