annotate baredsc_combine_1d.xml @ 1:050cf43887d3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit 576069ce2296ef58daa8a4e03c993d5900608c4c
author iuc
date Mon, 16 Oct 2023 14:00:49 +0000
parents c32347702e12
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c32347702e12 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_1d" name="Combine multiple 1D 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>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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9 </edam_operations>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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10 <xrefs>
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11 <xref type="bio.tools">baredsc</xref>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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12 </xrefs>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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13 <expand macro="requirements"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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14 <command detect_errors="exit_code"><![CDATA[
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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15 ## Create symlinks
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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16 #for $i, $output in enumerate($MCMC.outputs):
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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17 ln -s '$output' '${i}.npz' &&
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18 #end for
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19
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20 ## Run
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21 combineMultipleModels_1d
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22 ## Required inputs:
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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23 @REQUIRED_INPUTS_1D@
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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_1D@
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31 ## Plots
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32 @PLOTS@
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33 @PRETTYBINS_1D@
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34 ## Advanced
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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35 @ADVANCED_COMMON_X@
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36 ## Outputs
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37 --figure baredSC.$plots.image_file_format &&
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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38 mkdir output &&
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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39 @ORDER_OUTPUTS_1D@
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40 ]]></command>
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41 <inputs>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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42 <expand macro="macro_input_counts"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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43 <expand macro="macro_single_gene"/>
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44 <expand macro="macro_filter_cells"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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45 <section name="MCMC" title="MCMC parameters">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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46 <expand macro="combine_outputs" d="1" />
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47 <expand macro="macro_MCMC_params_common_axis" axis="x" />
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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48 <expand macro="macro_scale_seed"/>
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49 </section>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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50 <section name="plots" title="Customize plots">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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51 <expand macro="macro_plots"/>
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52 <expand macro="macro_prettybins_1d"/>
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53 </section>
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54 <section name="advanced" title="Advanced parameters" expanded="false">
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55 <expand macro="macro_advanced_common_axis" axis="x"/>
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56 <expand macro="macro_advanced_evidence"/>
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57 </section>
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58 </inputs>
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59 <outputs>
1
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60 <data format="tabular" name="pdf" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: PDF with error bar" from_work_dir="output/baredSC_pdf.txt">
0
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61 <actions>
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62 <action name="column_names" type="metadata" default="x,low,mean,high,median" />
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
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63 </actions>
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64 </data>
1
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65 <data format="png" name="plot" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: plot" from_work_dir="baredSC">
0
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66 <change_format>
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67 <when input="plots.image_file_format" value="png" format="png" />
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68 <when input="plots.image_file_format" value="svg" format="svg" />
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69 <when input="plots.image_file_format" value="pdf" format="pdf" />
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70 </change_format>
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71 </data>
1
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72 <collection type="list" name="other_outputs" label="${tool.name} on $getVar('input_counts.input', $getVar('input_counts.inputAnnData', 'shouldNeverHappen')).element_identifier for ${geneColName}: plots and txt">
0
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73 <discover_datasets pattern="baredSC_(?P&lt;identifier_0&gt;\S+)\.(?P&lt;ext&gt;.*)"/>
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74 </collection>
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75 </outputs>
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76 <tests>
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77 <!-- First test -->
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78 <test>
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79 <conditional name="input_counts">
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80 <param name="filetype" value="tabular"/>
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81 <param name="input" value="nih3t3_generated_2d_2.txt"/>
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82 </conditional>
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83 <param name="geneColName" value="0.5_0_0_0.5_x"/>
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84 <section name="MCMC">
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85 <param name="outputs" value="small_1gauss.npz,small_2gauss.npz"/>
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86 <param name="nx" value="10"/>
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87 </section>
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88 <section name="plots">
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89 <param name="title" value="first gene combine 1 and 2 gauss"/>
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90 <param name="prettyBins" value="100"/>
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91 </section>
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92 <!--In the next output pdf means probability density function-->
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93 <output name="pdf" ftype="tabular">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
94 <assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
95 <has_text_matching expression="x\s+low\s+mean\s+high\s+median"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
96 <has_n_lines n="101"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
97 <has_line_matching expression="0\.0125\s+0\.12[0-9]+\s+0\.37[0-9]+\s+0\.64[0-9]+\s+0\.33[0-9]+"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
98 </assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
99 </output>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
100 <output name="plot" ftype="png">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
101 <assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
102 <has_size value="244510" delta="20000"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
103 </assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
104 </output>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
105 <output_collection name="other_outputs" count="6" type="list">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
106 <element name="individuals" ftype="png">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
107 <assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
108 <has_size value="120034" delta="10000"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
109 </assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
110 </element>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
111 <element name="with_posterior" ftype="png">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
112 <assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
113 <has_size value="253397" delta="20000"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
114 </assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
115 </element>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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116 <element name="posterior_per_cell" ftype="txt">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
117 <assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
118 <has_n_lines n="2362"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
119 <has_line_matching expression="mu\s+sd"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
120 </assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
121 </element>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
122 <element name="posterior_andco" ftype="png">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
123 <assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
124 <has_size value="213773" delta="10000"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
125 </assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
126 </element>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
127 <element name="posterior_individuals" ftype="png">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
128 <assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
129 <has_size value="108794" delta="10000"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
130 </assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
131 </element>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
132 <element name="means" ftype="txt">
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
133 <assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
134 <has_n_lines n="15001"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
135 </assert_contents>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
136 </element>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
137 </output_collection>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
138 <assert_stdout>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
139 <has_text text="You have 2361 cells."/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
140 <has_text text="Using 12 samples from output 0."/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
141 <has_text text="Using 1 samples from output 0."/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
142 </assert_stdout>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
143 </test>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
144 </tests>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
diff changeset
145 <expand macro="helpcitations"/>
c32347702e12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc commit dad42d788f7407976a67ed50cc886ebe79740e32
iuc
parents:
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146 </tool>