Mercurial > repos > iuc > baredsc_combine_2d

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 55a4f3540558731fb47bf130c6a8984fa6f6ec9a
author iuc
date Tue, 26 Mar 2024 15:11:58 +0000
parents 1d77986f9ddc
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1 <tool id="baredsc_combine_2d" name="Combine multiple 2D Models" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description>from baredSC</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam_topics"/>
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7 <edam_operations>
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8 <edam_operation>operation_2495</edam_operation>
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9 <edam_operation>operation_3463</edam_operation>
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10 </edam_operations>
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11 <xrefs>
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12 <xref type="bio.tools">baredsc</xref>
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13 </xrefs>
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14 <expand macro="requirements"/>
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15 <command detect_errors="exit_code"><![CDATA[
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16 ## Create symlinks
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17 #for $i, $output in enumerate($MCMC.outputs):
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18 ln -s '$output' '${i}.npz' &&
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19 #end for
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21 combineMultipleModels_2d
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22 ## Required inputs:
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23 @REQUIRED_INPUTS_2D@
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24
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25 ## Filter cells
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26 @FILTER_CELLS@
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27
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28 @COMBINE_OUTPUTS@
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29 ## MCMC
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30 @MCMC_2D@
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31 ## Plots
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32 @PLOTS@
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33 @PRETTYBINS_SPLITY_COLORSCALE_2D@
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34 ## Advanced
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35 @ADVANCED_COMMON_X@
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36 @ADVANCED_COMMON_COMPLEMENT_2D@
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37 $advanced.getPVal
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38 ## Outputs
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39 --figure baredSC.$plots.image_file_format &&
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40 mkdir output &&
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41 @ORDER_OUTPUTS_2D@
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42 ]]></command>
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43 <inputs>
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44 <expand macro="macro_input_counts"/>
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45 <expand macro="macro_two_genes"/>
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46 <expand macro="macro_filter_cells"/>
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47 <section name="MCMC" title="MCMC parameters">
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48 <expand macro="combine_outputs" d="2" />
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49 <expand macro="macro_MCMC_params_common_axis" axis="x" />
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50 <expand macro="macro_MCMC_params_common_axis" axis="y" />
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51 <expand macro="macro_scale_seed"/>
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52 </section>
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53 <section name="plots" title="Customize plots">
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54 <expand macro="macro_plots"/>
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55 <expand macro="macro_prettybins_axis" axis="x"/>
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56 <expand macro="macro_prettybins_axis" axis="y"/>
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57 <expand macro="macro_colorscale"/>
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58 <expand macro="macro_splity"/>
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59 </section>
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60 <section name="advanced" title="Advanced parameters" expanded="false">
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61 <param argument="--getPVal" type="boolean" truevalue="--getPVal" falsevalue="" checked="false" label="Use less samples to get an estimation of the p-value."/>
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62 <expand macro="macro_advanced_common_axis" axis="x" default_osamppdf="4"/>
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63 <expand macro="macro_advanced_common_axis" axis="y" default_osamppdf="4"/>
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64 <expand macro="macro_advanced_evidence"/>
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65 <expand macro="macro_scaleprior"/>
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66 </section>
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67 </inputs>
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68 <outputs>
1
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69 <data format="tabular" name="pdf2d" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: mean PDF in matrix format" from_work_dir="output/baredSC_pdf2d.txt"/>
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70 <data format="tabular" name="pdf2d_flat" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: PDF with error bar, one bin per line" from_work_dir="output/baredSC_pdf2d_flat.txt">
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71 <actions>
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72 <action name="column_names" type="metadata" default="x,y,low,mean,high,median" />
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73 </actions>
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74 </data>
1
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75 <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: plot" from_work_dir="baredSC">
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76 <change_format>
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77 <when input="plots.image_file_format" value="png" format="png" />
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78 <when input="plots.image_file_format" value="svg" format="svg" />
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79 <when input="plots.image_file_format" value="pdf" format="pdf" />
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80 </change_format>
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81 </data>
1
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82 <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: plots and txt">
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83 <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
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84 </collection>
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85 </outputs>
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86 <tests>
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87 <!-- First test -->
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88 <test>
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89 <conditional name="input_counts">
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90 <param name="filetype" value="tabular"/>
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91 <param name="input" value="nih3t3_generated_2d_2.txt"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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92 </conditional>
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93 <param name="geneXColName" value="0.5_0_0_0.5_x"/>
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94 <param name="geneYColName" value="0.5_0_0_0.5_y"/>
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iuc
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95 <section name="MCMC">
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96 <param name="outputs" value="2d_small_1gauss.npz,2d_small_2gauss.npz"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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97 <param name="nx" value="10"/>
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98 <param name="ny" value="12"/>
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99 </section>
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100 <section name="plots">
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101 <param name="prettyBinsx" value="20"/>
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102 <param name="prettyBinsy" value="20"/>
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103 </section>
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104 <output name="pdf2d" ftype="tabular">
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105 <assert_contents>
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106 <has_n_lines n="21"/>
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107 </assert_contents>
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108 </output>
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109 <output name="pdf2d_flat" ftype="tabular">
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110 <assert_contents>
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111 <has_text_matching expression="x\s+y\s+low\s+mean\s+high\s+median"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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112 <has_n_lines n="401"/>
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113 </assert_contents>
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114 </output>
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115 <output name="plot" ftype="png">
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116 <assert_contents>
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117 <has_size value="37414" delta="3000"/>
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118 </assert_contents>
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119 </output>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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120 <output_collection name="other_outputs" count="3" type="list">
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iuc
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121 <element name="corr" ftype="txt">
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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122 <assert_contents>
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iuc
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123 <has_n_lines n="2"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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124 <has_line_matching expression="mean\tmedian\tlow\thigh"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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125 <has_text_matching expression="0\.9[0-9]+\s+0\.9[0-9]+\s+0\.8[0-9]+\s+0\.9[0-9]+"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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126 </assert_contents>
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iuc
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127 </element>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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128 <element name="individuals" ftype="png">
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129 <assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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130 <has_size value="56721" delta="5000"/>
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iuc
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131 </assert_contents>
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132 </element>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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133 <element name="median" ftype="png">
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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134 <assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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135 <has_size value="37412" delta="4000"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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136 </assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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137 </element>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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138 </output_collection>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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139 </test>
2
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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diff changeset
140 <!-- Second test -->
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141 <test>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
iuc
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diff changeset
142 <conditional name="input_counts">
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
iuc
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143 <param name="filetype" value="tabular"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
iuc
parents: 1
diff changeset
144 <param name="input" value="nih3t3_generated_2d_2.txt"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
iuc
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diff changeset
145 </conditional>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
iuc
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diff changeset
146 <param name="geneXColName" value="0.5_0_0_0.5_x"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
iuc
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diff changeset
147 <param name="geneYColName" value="0.5_0_0_0.5_y"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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diff changeset
148 <section name="MCMC">
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iuc
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diff changeset
149 <param name="outputs" value="2d_small_1gauss.npz,2d_small_2gauss.npz"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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diff changeset
150 <param name="nx" value="10"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
iuc
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diff changeset
151 <param name="ny" value="12"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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diff changeset
152 </section>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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153 <section name="plots">
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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diff changeset
154 <param name="prettyBinsx" value="5"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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155 <param name="prettyBinsy" value="5"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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156 </section>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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diff changeset
157 <section name="advanced">
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158 <param name="getPVal" value="true"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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159 </section>
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160 <output name="pdf2d" ftype="tabular">
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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161 <assert_contents>
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162 <has_n_lines n="6"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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163 </assert_contents>
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164 </output>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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165 <output name="pdf2d_flat" ftype="tabular">
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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166 <assert_contents>
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167 <has_text_matching expression="x\s+y\s+low\s+mean\s+high\s+median"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
iuc
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168 <has_n_lines n="26"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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169 </assert_contents>
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diff changeset
170 </output>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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171 <output name="plot" ftype="png">
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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172 <assert_contents>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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173 <has_size value="35696" delta="3000"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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174 </assert_contents>
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175 </output>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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176 <output_collection name="other_outputs" count="3" type="list">
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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diff changeset
177 <element name="corr" ftype="txt">
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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178 <assert_contents>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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diff changeset
179 <has_n_lines n="2"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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180 <has_line_matching expression="mean\tmedian\tlow\thigh\tpval\terror"/>
1d77986f9ddc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 01d58fe886f6ab256b6eb8d4a65b978f81b81262
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181 <has_text_matching expression="0\.9[0-9]+\s+0\.9[0-9]+\s+0\.9[0-9]+\s+0\.9[0-9]+\s+0\.007[0-9]+\s+0\.007[0-9]+"/>
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182 </assert_contents>
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183 </element>
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184 <element name="individuals" ftype="png">
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185 <assert_contents>
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186 <has_size value="73051" delta="7000"/>
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187 </assert_contents>
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188 </element>
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189 <element name="median" ftype="png">
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190 <assert_contents>
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191 <has_size value="35686" delta="4000"/>
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192 </assert_contents>
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193 </element>
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194 </output_collection>
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195 <assert_stdout>
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196 <has_text text="Sampling 127 independent samples."/>
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197 </assert_stdout>
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198 </test>
0
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199 </tests>
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200 <expand macro="helpcitations"/>
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201 </tool>