Mercurial > repos > iuc > baredsc_combine_2d

annotate baredsc_combine_2d.xml @ 1:ae969fdb8442 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 576069ce2296ef58daa8a4e03c993d5900608c4c
author iuc
date Mon, 16 Oct 2023 14:01:47 +0000
parents 239193b96d72
children 1d77986f9ddc
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239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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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 ## Outputs
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38 --figure baredSC.$plots.image_file_format &&
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39 mkdir output &&
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40 @ORDER_OUTPUTS_2D@
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41 ]]></command>
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42 <inputs>
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43 <expand macro="macro_input_counts"/>
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44 <expand macro="macro_two_genes"/>
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45 <expand macro="macro_filter_cells"/>
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46 <section name="MCMC" title="MCMC parameters">
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47 <expand macro="combine_outputs" d="2" />
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48 <expand macro="macro_MCMC_params_common_axis" axis="x" />
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49 <expand macro="macro_MCMC_params_common_axis" axis="y" />
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50 <expand macro="macro_scale_seed"/>
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51 </section>
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52 <section name="plots" title="Customize plots">
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53 <expand macro="macro_plots"/>
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54 <expand macro="macro_prettybins_axis" axis="x"/>
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55 <expand macro="macro_prettybins_axis" axis="y"/>
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56 <expand macro="macro_colorscale"/>
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57 <expand macro="macro_splity"/>
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58 </section>
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59 <section name="advanced" title="Advanced parameters" expanded="false">
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60 <expand macro="macro_advanced_common_axis" axis="x" default_osamppdf="4"/>
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61 <expand macro="macro_advanced_common_axis" axis="y" default_osamppdf="4"/>
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62 <expand macro="macro_advanced_evidence"/>
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63 <expand macro="macro_scaleprior"/>
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64 </section>
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65 </inputs>
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66 <outputs>
1
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67 <data format="tabular" name="pdf2d" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: mean PDF in matrix format" from_work_dir="output/baredSC_pdf2d.txt"/>
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68 <data format="tabular" name="pdf2d_flat" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: PDF with error bar, one bin per line" from_work_dir="output/baredSC_pdf2d_flat.txt">
0
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69 <actions>
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70 <action name="column_names" type="metadata" default="x,y,low,mean,high,median" />
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71 </actions>
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72 </data>
1
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73 <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: plot" from_work_dir="baredSC">
0
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74 <change_format>
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75 <when input="plots.image_file_format" value="png" format="png" />
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76 <when input="plots.image_file_format" value="svg" format="svg" />
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77 <when input="plots.image_file_format" value="pdf" format="pdf" />
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78 </change_format>
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79 </data>
1
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80 <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneXColName} and ${geneYColName}: plots and txt">
0
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81 <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
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82 </collection>
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83 </outputs>
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84 <tests>
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85 <!-- First test -->
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86 <test>
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87 <conditional name="input_counts">
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88 <param name="filetype" value="tabular"/>
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89 <param name="input" value="nih3t3_generated_2d_2.txt"/>
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90 </conditional>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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91 <param name="geneXColName" value="0.5_0_0_0.5_x"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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parents:
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92 <param name="geneYColName" value="0.5_0_0_0.5_y"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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93 <section name="MCMC">
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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94 <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
iuc
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95 <param name="nx" value="10"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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parents:
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96 <param name="ny" value="12"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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97 </section>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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98 <section name="plots">
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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99 <param name="prettyBinsx" value="20"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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100 <param name="prettyBinsy" value="20"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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101 </section>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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102 <output name="pdf2d" ftype="tabular">
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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103 <assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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104 <has_n_lines n="21"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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105 </assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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106 </output>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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107 <output name="pdf2d_flat" ftype="tabular">
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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108 <assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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109 <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
iuc
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110 <has_n_lines n="401"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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111 </assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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112 </output>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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113 <output name="plot" ftype="png">
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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114 <assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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115 <has_size value="37414" delta="3000"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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116 </assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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117 </output>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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118 <output_collection name="other_outputs" count="3" type="list">
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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119 <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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120 <assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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121 <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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122 <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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123 <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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124 </assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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125 </element>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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126 <element name="individuals" ftype="png">
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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127 <assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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128 <has_size value="56721" delta="5000"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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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 </element>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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131 <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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132 <assert_contents>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
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133 <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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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 </element>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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136 </output_collection>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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137 </test>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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138 </tests>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
139 <expand macro="helpcitations"/>
239193b96d72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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140 </tool>